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At least 685 records · Page 38

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↗

A legacy of fire emerges from multiple disturbances to most shape microbial and nitrogen dynamics in a deciduous forest

Healthy forests are vital components of terrestrial ecosystems for their raw materials, high biodiversity, cycling of nutrients, and potential to sequester carbon. However, these ecosystems are sensitive to disturbances, and anthropogenic activities pose a serious threat to forest ecosystems globally. For example, human activities have dramatically altered multiple historical disturbance regimes in forests, including suppressing fire, increasing the density of large herbivores, and reducing the size of canopy gaps, among other disturbances. Such disturbances can have dramatic impacts on microbially-mediated forest soil functions, but more research is needed to determine the collective impacts of these disturbances. In this study, we investigated the interactive effects of disturbances, namely the legacies of fire, large herbivore densities, and canopy gap creation, in a deciduous forest soil. We determined that forest floor and mineral soil carbon and nitrogen pools were shaped by multiple disturbances, but fire was more influential than the other disturbances. The abundance of several functionally-relevant microbial taxa were significantly impacted by fire, and the effect was more pronounced in the mineral soil than in the forest floor. Together, these findings demonstrate that multiple disturbances, especially a legacy of fire, exerts long-term control over soil carbon, nitrogen and microbial dynamics in a deciduous forest system.

59 BASIC BIOLOGICAL SCIENCES↗

Assessing microbial community patterns under incipient soil formation from basalt

Microbial dynamics drive the biotic machinery of early soil evolution. However, integrated knowledge of microbial community establishment, functional associations, and community assembly processes in incipient soil is lacking. This study presents a novel approach of combining microbial phylogenetic profiling, functional predictions, and community assembly processes to analyze drivers of microbial community establishment in an emerging soil system. Rigorous sub-meter sampling of a basalt-soil lysimeter after two years of irrigation revealed the contrasting depth-dependent distribution patterns of soil parameters and community diversity. Phylogenetic analysis of 16S rRNA gene indicated the presence of diverse bacterial and archaeal phyla, with high relative abundance of Actinobacteria on the surface and a consistently high abundance of Proteobacteria at all depths. Predicted functional gene analysis suggested dominant autotrophy signatures, evidence of an incomplete nitrogen cycle, and predicted enzymes of iron (III) to iron (II) conversion followed by intracellular uptake, transport, and regulation. Null modeling revealed microbial community assembly predominantly governed by variable selection. The relative influence of the variable selection decreased with depth, indicating unique and relatively harsh environmental conditions near the surface and more benign conditions with depth. Additionally, high levels of dispersal influenced community composition near the center of the domain, suggesting that spatial processes interact with deterministic selection imposed by the environment. Characterizing the complexity in incipient soils can advance research insights about microbial community diversity and assembly in other incipient systems (e.g., transformation of marginal soils, or soils recovering from disturbances such as fire, erosion, intensive agricultural practices, or contamination).

Sengupta, Aditi↗

Growth rate as a link between microbial diversity and soil biogeochemistry

The growth rate of a microorganism is a simple yet profound way to quantify its impact on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production, and element transformation, some of the many ways that organisms affect Earth’s ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favorable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining ‘omics and stable isotope probing enable sensitive measurements of growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions, and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake, and ecosystem productivity. Finally, measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗

Nearest-Neighbor Machine Learning Feature Selection for Interpretation of Microbial Molecular Signatures from Isotope Ratio Mass Spectrometry Data

Mass spectrometry (MS) promises to be a powerful tool for potential biosignature detection during astrobiological missions on ocean worlds in our solar system. Accurate and generalizable machine learning methods could enhance science return on investment by predicting seawater chemistry and classifying isotopic biosignatures, either as a signature consistent with microbial life (biotic) or as a novelty (unclassified/unique). However, machine learning models are likely to be complex and involve interactions between MS features, making biosignatures difficult to interpret. Feature selection methods provide biological and chemical context that help interpret the mechanisms of machine learning models, but these methods also need the ability to detect complex interactions. Previously, we developed a machine learning feature selection algorithm called nearest-neighbor projected distance regression (NPDR) that has the ability to identify important model features that involve complex interactions and automatically reduce correlation and the dimensionality in a high-dimensional variable space. The standard distance metrics used in NPDR – Manhattan and Euclidean – assume the multivariate data are isotropic, which is often violated in real data due to differences in the covariance between variables. Thus, we extend NPDR to include a random forest distance, and other anisotropic distance metrics, for computing nearest neighbors. We also augment the isotope-ratio MS data with time-series features from the raw MS signal to improve biotic classification. We test NPDR on our novel experimental ocean world seawater analog MS data. We measure isotope fractionations of volatile CO 2 that could be measured in exospheres or plumes. Samples include baseline abiotic conditions using a range of possible seawater chemistry consistent with Europa and Enceladus, and biotic samples that include microbes in these seawaters. We use penalized NPDR with random forest proximity to identify interpretable microbial molecular signatures. We compare features with random forest importance, and we train a classifier that discriminates between biotic and abiotic samples with high accuracy. These ML-trained ocean-world analog MS data could be used to assist in identifying biosignatures during future missions.

geochemistry↗

Decomposition responses to climate depend on microbial community composition

Significance We overcame the difficulty of disentangling biotic and abiotic effects on decomposition by using the largest field-based reciprocal transplant experiment to date. We showed that decomposition responses to climate depend on the composition of microbial communities, which is not considered in terrestrial carbon models. Microbial communities varied in their effects on both mass loss and types of carbon decomposed in an interactive manner not predicted by current theory. Contrary to the traditional paradigm, bacterial communities appeared to have a stronger impact on grassland litter decomposition rates than fungi. Furthermore, bacterial communities shifted more rapidly in response to changing climates than fungi. This information is critical to improving global terrestrial carbon models and predicting ecosystem responses to climate change.

Glassman, Sydney I.↗

Novel plant–microbe interactions: Rapid evolution of a legume–rhizobium mutualism in restored prairies

Abstract When plants colonize new habitats, the novel interactions they form with new mutualists or enemies can immediately affect plant performance. These novel interactions also may provoke rapid evolutionary responses and can be ideal scenarios for investigating how species interactions influence plant evolution. To explore how mutualists influence the evolution of colonizing plant populations, we capitalized on an experiment in which two former agricultural fields were seeded with identical prairie seed mixes in 2010. Six years later, we compared how populations of the legume Chamaecrista fasciculata from these sites and their original (shared) source population responded to nitrogen‐fixing rhizobia from the restoration sites in a greenhouse reciprocal cross‐inoculation experiment. We found that the two populations differed both from their original source population and from each other in the benefits they derive from rhizobia, and that one population has evolved reduced allocation to rhizobia (i.e. forms fewer rhizobium‐housing nodules). Synthesis . Our results suggest that these plant populations have evolved different ways of interacting with rhizobia, potentially in response to differences in rhizobium quality between sites. Our study illustrates how microbial mutualists may shape plant evolution in new environments and highlights how variation in microbial mutualists potentially may select for different evolutionary strategies in plant hosts.

Magnoli, Susan M.↗

RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization

To survive diverse host environments, the human pathogen Streptococcus pneumoniae must prevent its self-produced, extremely high levels of peroxide from reacting with intracellular iron. However, the regulatory mechanism(s) by which the pneumococcus accomplishes this balance remains largely enigmatic, as this pathogen and other related streptococci lack all known redox-sensing transcription factors. Here we describe a two-component-derived response regulator, RitR, as the archetype for a novel family of redox sensors in a subset of streptococcal species. We show that RitR works to both repress iron transport and enable nasopharyngeal colonization through a mechanism that exploits a single cysteine (Cys128) redox switch located within its linker domain. Biochemical experiments and phylogenetics reveal that RitR has diverged from the canonical two-component virulence regulator CovR to instead dimerize and bind DNA only upon Cys128 oxidation in air-rich environments. Atomic structures show that Cys128 oxidation initiates a “helical unravelling” of the RitR linker region, suggesting a mechanism by which the DNA-binding domain is then released to interact with its cognate regulatory DNA. Expanded computational studies indicate this mechanism could be shared by many microbial species outside the streptococcus genus.

59 BASIC BIOLOGICAL SCIENCES↗

Microfossils in the Antarctic cold desert: Possible implications for Mars

In the Ross Desert of Antarctica, the principal life form is the cryptoendolithic microbial community in the near-surface layers of porous sandstone rocks. Biological, geological, and climatic factors interact in a complex and precarious balance, making life possible in an otherwise hostile environment. Once this balance is tipped, fossilization sets in. In the reverse case, new colonization of the rock surface may be initiated. As a result, fossilization is contemporary with modern life and both may be simultaneously present in a mosaic pattern. Also, different stages of fossilization are present. The process of fossilization takes place in a nonaquatic environment. If primitive life ever appeared on Mars, it is possible that with increasing aridity, life withdrew into an endolithic niche similar to that in the Antarctic desert. Fossilization in a nonaquatic environment may have set in with the result that traces of past life could be preserved. If such was the case, the study of the fossilization process in Antarctica may hold useful information for the analysis of Martian samples for microfossils.

Friedmann, E. I.↗

From viruses to protists: temperature response of the neglected components of microbial controls on peatland nutrient cycling

The response of plant-associated microbial communities to rising temperatures likely plays a key role in global Carbon (C) and Nitrogen (N) biogeochemical cycles. Mosses of the genus Sphagnum, in particular, sequester 25% of all terrestrial C as recalcitrant peat. However, their ability to sequester C is mediated by interactions with microbes that fix N and pass it to the moss to grow in otherwise oligotrophic systems. Two important biotic controls on this processes are likely to respond to rising temperatures –predation by protists and infections by viruses– but whether and how this might occur is not well understood. This proposal addressed these questions using a combination of genomics and mathematical modeling with both field data from whole-ecosystem warming experiments, and laboratory-based microcosm experiments. We have discovered 1) mechanistic links between cell traits and thermal performance in protists, which 2) enabled predictions from populations to ecosystems, 3) we have identified eco-phenotypic feedbacks that determine protist–bacterial predator–prey dynamics, 4) have documented concomitant compositional and trait shifts in protist communities with warming in the field, 5) revealed consistent interactive effects of temperature and nutrients on bacterial and protist communities; 6) characterized the Sphagnum virome, and 7) made modeling predictions on its implications for thermal responses of microbial communities in peatlands globally. This award also substantially strengthened U.S. scientific capacity and workforce development.

Gibert, Jean Philippe [Duke University]↗

Systems Analysis of the Physiological and Molecular Mechanisms of Sorghum Nitrogen Use Efficiency, Water Use Efficiency and Interactions with the Soil Microbiome (Final Report for DE-SC0014395)

The specific project objectives were to: 1) Conduct deep census surveys of root microbiomes concurrent with phenotypic characterizations of a diverse panel of sorghum genotypes across multiple years to define the microbes associated with the most productive lines under drought and low nitrogen conditions. 2) Associate systems-level genotypic, microbial, and environmental factors with improved sorghum performance using robust statistical approaches. 3) Develop culture collections of sorghum root/leaf associated microbes that recapitulate root-enriched sequences defined in the census. 4) Perform controlled environment experiments for in-depth characterization and hypothesis testing of G sorghum x G microbe x E interactions . Validate physiological mechanisms, map genetic loci for stress tolerance, and determine the persistence of optimal microbial strains under greenhouse and field conditions.

59 BASIC BIOLOGICAL SCIENCES↗

Bacillus licheniformis in geogenic dust induces inflammation in respiratory epithelium

Highlights: • Earth-derived geogenic dust exposure can lead to infections in the human airway. • Spore-forming Bacillus licheniformis is present in rural geogenic PM{sub 10.} • Heat-treating geogenic dust removes its stimulatory effects on airway epithelium. • High airway IL-6 and IL-8 levels are induced by live Bacillus licheniformis. • Bacillus licheniformis may exacerbate infections associated with dust exposure. Exposure to environmental geogenic (or earth-derived) dust can lead to more frequent and severe infections in the human airway. Particulate matter < 10 µm (PM{sub 10}) is the component of air pollution that is commonly associated with the exacerbation of respiratory diseases. We have previously demonstrated that mice exposed to geogenic dust PM{sub 10} experienced an exacerbation of inflammatory responses to influenza A virus. Whether geogenic dust PM{sub 10} also exacerbates respiratory bacterial infection is not yet known, nor are the components of the dust that drive these responses. We treated airway bronchial epithelial cells (NuLi-1) with UV-irradiated geogenic dust PM{sub 10} from six remote Western Australian towns. High levels of IL-6 and IL-8 production were observed, as well as persistent microbial growth. 16 S rRNA sequencing of the growth identified the microbe as Bacillus licheniformis, a spore-forming, environmentally abundant bacterium. We next investigated the interaction of B. licheniformis with respiratory epithelium in vitro to determine whether this exacerbated infection with a bacterial respiratory pathogen (non-typeable Haemophilus influenzae, NTHi). Heat treatment (100 °C) of all PM{sub 10} samples eliminated B. licheniformis contamination and reduced epithelial inflammatory responses, suggesting that heat-labile and/or microbial factors were involved in the host response to geogenic dust PM{sub 10}. We then exposed NuLi-1 epithelium to increasing doses of the isolated Bacillus licheniformis (multiplicity of infection of 10:1, 1:1 or 0.1:1 bacteria: cells) for 1, 3, and 24 h. B. licheniformis and NTHi infection (association and invasion) was assessed using a standard gentamicin survival assay, and epithelial release of IL-6 and IL-8 was measured using a bead based immunoassay. B. licheniformis was cytotoxic to NuLi-1 cells at 24 h. At 3 h post-challenge, B. licheniformis elicited high IL-6 and IL-8 inflammatory responses from NuLi-1 cells compared with cells treated with heat-treated geogenic dust PM{sub 10} (p < 0.0001). Whilst treatment of cells with B. licheniformis increased inflammation, this did not make the cells more susceptible to NTHi infection. This study highlights that geogenic dust PM{sub 10} can harbour viable bacterial spores that induce inflammation in respiratory epithelium. The impact on respiratory health from inhalation of bacterial spores in PM{sub 10} in arid environments may be underestimated. Further investigation into the contribution of B. licheniformis and the wider dust microbiome to respiratory infection is warranted.

54 ENVIRONMENTAL SCIENCES↗

Flux, Impact, and Fate of Halogenated Xenobiotic Compounds in the Gut

Humans and their associated microbiomes are exposed to numerous xenobiotics through drugs, dietary components, personal care products as well as environmental chemicals. Most of the reciprocal interactions between the microbiota and xenobiotics, such as halogenated compounds, occur within the human gut harboring diverse and dense microbial communities. Here, we provide an overview of the flux of halogenated compounds in the environment, and diverse exposure routes of human microbiota to these compounds. Subsequently, we review the impact of halogenated compounds in perturbing the structure and function of gut microbiota and host cells. In turn, cultivation-dependent and metagenomic surveys of dehalogenating genes revealed the potential of the gut microbiota to chemically alter halogenated xenobiotics and impact their fate. Finally, we provide an outlook for future research to draw attention and attract interest to study the bidirectional impact of halogenated and other xenobiotic compounds and the gut microbiota.

59 BASIC BIOLOGICAL SCIENCES↗

A holistic framework integrating plant-microbe-mineral regulation of soil bioavailable nitrogen

Abstract Soil organic nitrogen (N) is a critical resource for plants and microbes, but the processes that govern its cycle are not well-described. To promote a holistic understanding of soil N dynamics, we need an integrated model that links soil organic matter (SOM) cycling to bioavailable N in both unmanaged and managed landscapes, including agroecosystems. We present a framework that unifies recent conceptual advances in our understanding of three critical steps in bioavailable N cycling: organic N (ON) depolymerization and solubilization; bioavailable N sorption and desorption on mineral surfaces; and microbial ON turnover including assimilation, mineralization, and the recycling of microbial products. Consideration of the balance between these processes provides insight into the sources, sinks, and flux rates of bioavailable N. By accounting for interactions among the biological, physical, and chemical controls over ON and its availability to plants and microbes, our conceptual model unifies complex mechanisms of ON transformation in a concrete conceptual framework that is amenable to experimental testing and translates into ideas for new management practices. This framework will allow researchers and practitioners to use common measurements of particulate organic matter (POM) and mineral-associated organic matter (MAOM) to design strategic organic N-cycle interventions that optimize ecosystem productivity and minimize environmental N loss.

Environmental Sciences & Ecology↗

MR13A-3183: Microbial and Geochemical Characterization of Groundwater: Implications for Underground Hydrogen Storage Leakage

Underground hydrogen storage (UHS) in geological formations is a key element of the clean energy transition as it enables the decarbonization of the transportation and industrial sectors by decoupling hydrogen production and storage. UHS has many benefits, including low cost, much wider availability, large storage capacity, well-established infrastructure, and increased safety because of geological sealing capabilities. However, the impact of hydrogen (H2) biogeochemical interactions in the presence of subsurface microorganisms is largely neglected from UHS perspectives. These interactions might affect the effectiveness of storage and can even cause H2 to leak into the shallow aquifers. Leakage of H2 into groundwater can change the geochemistry and induce several microbial-driven processes. Microorganisms, such as sulfate-reducers, are naturally abundant in groundwater and consume H2 to produce hydrogen sulfide (H2S), which can contaminate the freshwater drinking groundwater and cause damage to infrastructure. Hydrogen leakage can also trigger microbial reactions responsible for metal mobility, which can impact the water quality. However, the kinetics of these reactions and the temporal impact of hydrogen leakage in groundwater are still unknown. Therefore, a time series hydrogen-groundwater interaction experiment was conducted, and the changes in fluid chemistry and headspace gas composition will be analyzed along with DNA sequencing results to understand the extent and kinetics of biogeochemical reactions that occur if hydrogen leaks into groundwater. In the experiments, Ultra High Purity (UHP) hydrogen gas will be injected into glass vials with groundwater samples, for a designated time period. For each glass-sealed vial, 16S rRNA gene sequencing, IC, ICP-MS, and GC-TCD will be performed. The experiments provide insights into plausible impacts of hydrogen leakage into shallow drinking water aquifers.

Clark, Allison [West Virginia University (WVU)]↗

Nitrogen addition alters the relative importance of roots and mycorrhizal hyphae in regulating soil organic carbon accumulation in a karst forest

Plant belowground carbon (C) inputs from roots and associated mycorrhizal hyphae are increasingly recognized as critical drivers impacting soil organic C (SOC) pool. However, whether roots and mycorrhizal hyphae differentially regulate SOC formation and accumulation under elevated nitrogen (N) deposition remains to be addressed. Using an ingrowth-core technique, the relative contributions of roots and mycorrhizal hyphae to SOC accumulation were distinguished and quantified in a karst forest receiving three levels of N additions (control (0 kg N ha -1 yr -1 ), low N (150 kg N ha -1 yr -1 ) and high N (300 kg N ha -1 yr -1 )). Here our results showed that N addition stimulated SOC accumulation (indicated by the increase of both bulk SOC and mineral associated organic C fraction) influenced by both roots and hyphae, especially for higher N doses. Moreover, N addition increased the contribution of the root effect relative to the hyphal effect in the SOC accrual. The correlation analysis showed that, for the hyphal effect, the change in SOC content was solely and positively correlated with the change in protective mineral phases of SOC, but not with the microbial necromass. In contrast, for the root effect, the change in SOC content was significantly and positively correlated with the changes in both soil microbial C pump efficacy and protective mineral phases of SOC. These results suggest that roots and mycorrhizal hyphae may influence the accumulation of microbial necromass and the formation of mineral-organic associations in a different magnitude under enhanced N supply. These findings advance our understanding of the root-mycorrhizal interactions in mediating SOC dynamics in forests under future N deposition scenarios.

54 ENVIRONMENTAL SCIENCES↗

Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium

This narrative was used for the 4-member community modeling using MOPS medium for the bacteria isolated from Populus deltoides (PD). 10 bacterial strains isolated from PD were co-cultured as a synthetic microbial community in MOPS minimal medium. After 15 passages there were 4 members survived in MOPS medium. The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using MOPS medium. The FBA modeling was performed and the metabolites exchange among community members was proposed. The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.​1016/​j.​csbj.​2021.​03.​034

59 BASIC BIOLOGICAL SCIENCES↗

Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium

This narrative was used for the 3-member community modeling using R2A medium for the bacteria isolated from Populus deltoides (PD). 10 bacteiral strains isolated from PD were co-cultured as a synthetic microbial community in R2A complex medium. After 15 passages, there were 3 members survived in R2A medium. The genome of each community member was sequenced and uploaded into KBase for genome annotation and metabolic modeling. To simulate the metabolic interactions among the finally surviving community members, the individual metabolic models of each strain were merged into a compartmentalized community model, and then the community model was gapfilled using R2A medium. The FBA modeling was performed and the metabolites exchange among community members was proposed. The publication by Jia Wang, Dana L. Carper, Leah H. Burdick, Him Shrestha, Manasa Appidi, Paul E. Abraham, Collin M. Timm, Robert L. Hettich, Dale A. Pelletier, Mitchel J. Doktycz can be found here: https://doi.org/10.​1016/​j.​csbj.​2021.​03.​034

59 BASIC BIOLOGICAL SCIENCES↗