Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “plant microbiome”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Microbial drought resistance may destabilize soil carbon

Droughts are becoming more frequent and intense with climate change. As plants and microbes respond to drought, there may be consequences for the vast stocks of organic carbon stored in soils. If microbes sustain their activity under drought, soils could lose carbon, especially if inputs from plants decline. Empirical and theoretical studies reveal multiple mechanisms of microbial drought resistance, including tolerance and avoidance. Physiological responses allow microbes to acclimate to drought within minutes to days. Along with dispersal, shifts in community composition could allow microbiomes to maintain functioning despite drought. Microbes might also adapt to drier conditions through evolutionary processes. Together, these mechanisms could result in soil carbon losses larger than currently anticipated under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

IMAGINE BioSecurity: Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native Ecosystems

Project Goals: The Integrative Modeling and Genome-scale Engineering for Biosystems Security (IMAGINE BioSecurity) SFA project seeks to establish an understanding of the behavior of engineered microbes in controlled versus environmental conditions to predictively devise new strategies for responding to biological escape. To this end, the IMAGINE Team has established a plant-soil mesocosm platform to track and quantify the fate of industrial microbes in environmental systems and assess the efficacy of biocontainment constraints upon genetically engineered microbe escape frequency and the impact of industrial microbes upon native ecological microbiomes. Abstract Text: Genetically modified industrial production microbes and their associated bioproducts have emerged as an integral component of a sustainable bioeconomy. However, the rapid development of these innovative technologies raises biosecurity concerns, namely, the risk of environmental escape. Thus, the realization of a bioeconomy hinges not only on the development and deployment of microbial production hosts, but also on the development of secure biosystems and biocontainment designs. Current laboratory-based biocontainment testing systems do not accurately reflect complexities found in natural environments, necessitating an environmentally relevant analysis pipeline that allows for the detection of rare escapees, the effect of associated bio-products, and the impact on native ecologies. To this end, we have developed an approach that utilizes soil mesocosms and integrated systems analyses to evaluate the efficacy of novel biocontainment strategies and to assess the impact of production systems upon terrestrial microbiome dynamics. We demonstrate the utility of this approach by modeling a contamination with industrial microbial chasses versus their biocontained counterparts. Here we demonstrate the broad utility of this system by highlighting findings from both strains of Saccharomyces cerevisiae that are contained with an inducible toxin anti-toxin system, and stains of Escherichia coli that are contained via genomic recoding. The resultant data demonstrate that this system has broad utility across diverse microbial chassis and biocontainment strategies, enables us to track the fate of our contaminating microbe with high sensitivity in the soil, as well as monitor broader impacts of the perturbation on the underlying soil system. The findings presented here support the use of this mesocosm-based approach to assess the environmental impact of industrial microbes and to validate biocontainment strategies.

BASIC BIOLOGICAL SCIENCES,INORGANIC, ORGANIC, PHYS↗
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), 1–13. 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 OSTI2022

Landscape Topography and Regional Drought Alters Dust Microbiomes in the Sierra Nevada of California

Dust provides an ecologically significant input of nutrients, especially in slowly eroding ecosystems where chemical weathering intensity limits nutrient inputs from underlying bedrock. In addition to nutrient inputs, incoming dust is a vector for dispersing dust-associated microorganisms. While little is known about dust-microbial dispersal, dust deposits may have transformative effects on ecosystems far from where the dust was emitted. Using molecular analyses, we examined spatiotemporal variation in incoming dust microbiomes along an elevational gradient within the Sierra Nevada of California. We sampled throughout two dry seasons and found that dust microbiomes differed by elevation across two summer dry seasons (2014 and 2015), which corresponded to competing droughts in dust source areas. Dust microbial taxa richness decreased with elevation and was inversely proportional to dust heterogeneity. Likewise, dust phosphorus content increased with elevation. At lower elevations, early season dust microbiomes were more diverse than those found later in the year. The relative abundances of microbial groups shifted during the summer dry season. Furthermore, mutualistic fungal diversity increased with elevation, which may have corresponded with the biogeography of their plant hosts. Although dust fungal pathogen diversity was equivalent across elevations, elevation and sampling month interactions for the relative abundance, diversity, and richness of fungal pathogens suggest that these pathogens differed temporally across elevations, with potential implications for humans and wildlife. This study shows that landscape topography and droughts in source locations may alter the composition and diversity of ecologically relevant dust-associated microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Use of imaging and mass spectrometry-based capabilities to describe microbiome interactions (Q4 Performance Metric Report, 2021)

The LLNL “Microbes Persist” Soil Microbiome Scientific Focus Area (SFA) seeks to determine how microbial soil ecophysiology, population dynamics, and microbe-mineral-organic matter interactions regulate the persistence of microbial residues and formation of soil carbon (C). In much of our research, we use imaging, mass spectrometry, and related methods to study plantmicrobe-mineral interactions, viral and microbial particles from soil, and the signatures plant and microbial necromass contribute as part of soil organic matter (SOM). Our project’s signature techniques include NanoSIMS-enabled approaches (to understand cell-cell and OM-mineral interactions at the single cell and even viral particle scale), radiocarbon (14C) analyses (to determine both the age and turnover time of soil organic matter), and a suite of soil chemical characterization techniques we describe below, and collectively refer to as ‘Multi- dimensional SOM-mineral characterization’ (SEM, TEM, STXM, NEXAFS, NMR, FTICR-MS, LC-MS). In this report, we focus on how imaging, NMR, beamline and mass spectrometry approaches can deepen our understanding of soil microbiomes and their engagement with the soil matrix.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Connecting Nitrogen Transformations Mediated by the Rhizosphere Microbiome to Perennial Cropping System Productivity in Marginal Lands

The demand for energy from biofuel production is increasing, prompting concerns about the environmental impact and long-term sustainability of bioenergy cropping systems. These cropping systems will make up much of our future landscapes, and threaten to take the place of food cropping systems. Many life cycle analyses of bioenergy sustainability focus on carbon accrual and budgets, since they want to maximize carbon accrual while producing alternative fuel. Less attention has been given to nitrogen (N) dynamics in these systems. N is the most commonly limiting nutrient for plants, but applying nitrogen fertilizer- as we do for most cropping systems – is harmful to the environment, energetically costly, and produces greenhouse gases. In other words, adding nitrogen by fertilizer bioenergy systems could add to the very problems (climate change) it is trying to address. This is especially true for the areas that are proposed for bioenergy systems: marginal lands. These more degraded lands do not complete with food crops, but do have limited nitrogen. If we are to use these marginal lands for bioenergy, we need to understand the mechanisms regulating nutrient acquisition, and identify ways that bioenergy crops can get nitrogen in sustainable ways. Nutrient acquisition in the soil is performed by microbes in the root zone, or rhizosphere. Microbes can either mineralize nitrogen in the soil (from organic forms) or fix nitrogen from the air, in a process called nitrogen fixation. The goal of our project was thus to understand how the rhizosphere microbiome provides nutrients to bioenergy crops on marginal lands. We focus especially on the process of nitrogen fixation, since it has potential to get “fertilizer for free” that has much less environmental harm. We investigated this goal using sites from the DOE Great Lakes Bioenergy Research Center (GLBRC) in the upper Midwest, and associated lab and ‘omics methods. We group our findings into three major areas. First, we showed that nitrogen fixation, the conversion of N2 gas from the air to ammonium that is usable by plants, is performed in bioenergy soils, and benefits switchgrass crops. While more well-studied in leguminous plants, free-living nitrogen fixation can occur in some systems, and represents a potential opportunity to gain ‘free’ sustainable nitrogen source. We identified the nitrogen fixing bacteria that were most active in providing switchgrass with N, and showed that the drivers of nitrogen fixation occurred at a microscale; it is not well-predicted by bulk variables like soil moisture or plant phenology. Second, we showed that nitrogen fixation is not suppressed by long-term fertilizer. We expected that plentiful nitrogen would reduce the symbiotic relationship between nitrogen fixers and plants, and ‘downregulate’ fixation. We did not find evidence for this, either after long-term fertilizer in the field, or short-term fertilizer in the greenhouse. Finally, we identified the root exudates, carbon compounds that are emitted from the root, that best stimulate nitrogen fixation. We found that carbohydrates were better at stimulating fixation than organic acids. We expected these exudates to be emitted from the plant in periods of high N demand, but we found they are emitted when N is plentiful. This suggests that the stimulation of N fixation by plants is a passive process. Overall, we show that nitrogen fixation has potential to support bioenergy cropping system, and future management could develop ways to maximize it. However, this may not be best achieved via the plant – we found very little evidence of a ‘transactional’ system by which plants are controlling when and where nitrogen fixation is stimulated. It will be better to understand how management practices like planting and fertilizer application affect the microscale soil dynamics, which will determine nitrogen fixation rates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Microbial community composition controls carbon flux across litter types in early phase of litter decomposition

Leaf litter decomposition is a major carbon input to soil, making it a target for increasing soil carbon storage through microbiome engineering. We expand upon previous findings to show with multiple leaf litter types that microbial composition can drive variation in carbon flow from litter decomposition and specific microbial community features are associated with synonymous patterns of carbon flow among litter types. Although plant litter type selects for different decomposer communities, within a litter type, microbial composition drives variation in the quantity of dissolved organic carbon (DOC) measured at the end of the decomposition period. Bacterial richness was negatively correlated with DOC quantity, supporting our hypothesis that across multiple litter types there are common microbial traits linked to carbon flow patterns. Variation in DOC abundance (i.e. high versus low DOC) driven by microbial composition is tentatively due to differences in bacterial metabolism of labile compounds, rather than catabolism of non-labile substrates such as lignin. The temporal asynchrony of metabolic processes across litter types may be a substantial impediment to discovering more microbial features common to synonymous patterns of carbon flow among litters. Overall, our findings support the concept that carbon flow may be programmed by manipulating microbial community composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Mycorrhizal nutrient acquisition strategies shape tree competition and coexistence dynamics

Mycorrhizal fungi with different nutrient acquisition strategies influence plant species performance and physiology, thereby defining their trophic niche. This might drive resource competition dynamics that cumulatively impact tree species coexistence, but few manipulative experiments have directly tested this. Combining surveys and experiments in a modern coexistence theory framework, we tested how variation in mycorrhizal strategies and nutrient conditions affects plant competitive outcomes. We focused on two genera of co-occurring tree species with different mycorrhizal states: Acer (arbuscular mycorrhizal, AM) and Populus (dual mycorrhizal, but often considered predominantly ectomycorrhizal, EM). The EM and AM fungal responsiveness in Populus species varied with latitude and nitrogen (N) limitation. Host-specific soil microbiome conditioning and inorganic N fertilization combined to qualitatively affect coexistence outcomes. Lower N conditions favoured Populus over Acer trees, and N fertilization reversed this outcome for southern species, aligning with regional-scale forest mycorrhizal transitions. Results from the coexistence experiment also predict competitive exclusion between the tree species pairs, which could arise, in part, from their mycorrhizal differences and is consistent with alternative stable states in dominant forest mycorrhizal strategies. Such bistability appears in natural systems as a bimodal distribution of Populus vs. Acer tree species dominance using long-term forest inventory data. Synthesis: The magnitude and outcome of microbially mediated competition between Populus and Acer depends on soil nutrient availability, which likely relates to their mycorrhizal differentiation. These findings support the importance of mycorrhizal symbioses for contributing to large-scale biogeographical patterns of tree species trophic niche separation across soil resource gradients and bistability in forest mycorrhizal structure.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla

Plant-associated microbial communities have diverse phenotypic effects on their hosts that are only beginning to be revealed. We hypothesized that morpho-physiological variations in the tropical tree Tabebuia heterophylla, observed on different geological substrates, arise in part due to microbial processes in the rhizosphere. We characterized the microbiota of the rhizosphere and soil communities associated with T. heterophylla trees in high and low altitude sites (with varying temperature and precipitation) of volcanic, karst and serpentine geologies across Puerto Rico. We sampled 6 areas across the island in three geological materials including volcanic, serpentine and karst soils. Collection was done in 2 elevations (>450m and 0-300m high), that included 3 trees for each site and 4 replicate soil samples per tree of both bulk and rhizosphere. Genomic DNA was extracted from 144 samples, and 16S rRNA V4 sequencing was performed on the Illumina MiSeq platform. Proteobacteria, Actinobacteria, and Verrucomicrobia were the most dominant phyla, and microbiomes clustered by geological substrate and elevation. Volcanic samples were enriched in Verrucomicrobia; karst was dominated by nitrogen-fixing Proteobacteria, and serpentine sites harbored the most diverse communities, with dominant Cyanobacteria. Sites with similar climates but differing geologies showed significant differences on rhizobiota diversity and composition demonstrating the importance of geology in shaping the rhizosphere microbiota, with implications for the plant's phenotype. Our study sheds light on the combined role of geology and climate in the rhizosphere microbial consortia, likely contributing to the phenotypic plasticity of the trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Niche Partitioning of Microbial Communities at an Ancient Vitrified Hillfort: Implications for Vitrified Radioactive Waste Disposal

A pre-Viking era vitrified hillfort, Broborg, provides a habitat analogue for disposed radioactive waste glass and shows strong niche partitioning among the organisms involved in glass alteration. Microbes cannot be eliminated from radioactive waste disposal facilities and the consequences of bio-colonization must be understood. We use Broborg as a model system to inform what microbial processes might influence long-term radioactive waste glass durability by examining anthropogenic glass that has been subjected to bio-colonization for over 1,500 years. Scanning electron microscopy (SEM) images reveal the surficial biofilm structure, and chemical/mineralogy analysis in combination with deoxyribonucleic acid (DNA) sequencing of samples from the vitrified substrate, the adjacent soil, and the general topsoil provide insight into niche partitioning. The ancient glass niche supports a unique microbial community of bacteria, fungi, and protists that manifests the species response to local geochemical and mineralogical conditions. Communities from the geochemical niche associated with the glass are distinct and less diverse than soil communities. The microbiome of the glass and adjacent soil are dominated by lichens, lichen-associated microorganisms, and other epilithic, endolithic, and epigeic organisms. Pseudomonads dominate the prokaryotic communities on the vitrified material, but not the adjacent soil. In contrast, the general topsoil communities are enriched in plant rhizosphere organisms. Taxa associated with vitrification have bio-corrosive properties that could be detrimental to glass durability, including silicate mineral dissolution, extraction of essential elements, secretion of geochemically reactive organic acids, and dissolution induced by improved water retention. However, these stable long-term biofilms also possess a homeostatic function that could limit glass alteration. Overall, this study demonstrates the potential impacts that microbial colonization and niche partitioning can have on glass alteration and subsequent release of radionuclides from a disposal facility for vitrified radioactive waste.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Needle bacterial community structure across the species range of limber pine

Abstract Bacteria on and inside leaves can influence forest tree health and resilience. The distribution and limits of a tree species’ range can be influenced by various factors, with biological interactions among the most significant. We investigated the processes shaping the bacterial needle community across the species distribution of limber pine, a widespread Western conifer inhabiting a range of extreme habitats. We tested four hypotheses: (i) Needle community structure varies across sites, with site-specific factors more important to microbial assembly than host species selection; (ii) dispersal limitation structures foliar communities across the range of limber pine; (iii) the relative significance of dispersal and selection differs across sites in the tree species range; and (iv) needle age structures bacterial communities. We characterized needle communities from the needle surface and tissue of limber pine and co-occurring conifers across 16 sites in the limber pine distribution. Our findings confirmed that site characteristics shape the assembly of bacterial communities across the host species range and showed that these patterns are not driven by dispersal limitation. Furthermore, the strength of selection by the host varied by site, possibly due to differences in available microbes. Our study, by focusing on trees in their natural setting, reveals real needle bacterial dynamics in forests, which is key to understanding the balance between stochastic and deterministic processes in shaping forest tree-microbe interactions. Such understanding will be necessary to predict or manipulate these interactions to support forest ecosystem productivity or assist plant migration and adaptation in the face of global change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Impacts of The Wetland Sedge Carex aquatilis on Microbial Community and Methane Metabolisms

Microbial activity in the soil of wetlands is responsible for the emission of more methane to the atmosphere than all other natural sources combined. This microbial activity is heavily impacted by plant roots, which influence the microbial community by exuding organic compounds and by leaking oxygen into an otherwise anoxic environment. This study compared the microbial communities of planted and unplanted wetland soil from an Alaskan bog to elucidate how plant growth influences populations and metabolisms of methanogens and methanotrophs. A common boreal wetland sedge, Carex aquatilis, was grown in the laboratory and DNA samples were sequenced from the rhizosphere, unplanted bulk soil, and a simulated rhizosphere with oxygen input but no organic carbon. The abundance of both methanogens and methanotrophs were positively correlated with methane emissions. Among the methanotrophs, both aerobic and anaerobic methane oxidizing microbes were more common in the rhizosphere of mature plants than in unplanted soil, while facultative methanotrophs capable of utilizing either methane or other molecules became relatively less common. Furthermore, these trends indicate that the roots in this experiment created an environment which favored highly specialized microbial metabolisms over generalist approaches. One aspect of this specialized microbiome is the presence of both aerobic and anaerobic metabolisms, which indicates that oxygen is present but is a limiting resource controlling competition.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Development of modular expression across phylogenetically distinct diazotrophs

Diazotrophic bacteria can reduce atmospheric nitrogen into ammonia enabling bioavailability of the essential element. Many diazotrophs closely associate with plant roots increasing nitrogen availability, acting as plant growth promoters. These associations have the potential to reduce the need for costly synthetic fertilizers if they could be engineered for agricultural applications. However, despite the importance of diazotrophic bacteria, genetic tools are poorly developed in a limited number of species, in turn narrowing the crops and root microbiomes that can be targeted. Here, we report optimized protocols and plasmids to manipulate phylogenetically diverse diazotrophs with the goal of enabling synthetic biology and genetic engineering. Three broad-host-range plasmids can be used across multiple diazotrophs, with the identification of one specific plasmid (containing origin of replication RK2 and a kanamycin resistance marker) showing the highest degree of compatibility across bacteria tested. We then demonstrated modular expression by testing seven promoters and eleven ribosomal binding sites using proxy fluorescent proteins. Finally, we tested four small molecule inducible systems to report expression in three diazotrophs and demonstrated genome editing in Klebsiella michiganensis M5al.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Abstract Soil microbiomes are sensitive to current and previous soil conditions, and bacterial ‘bioindicators’ of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

The goal of this study is to explore interactions between plant detritus and the micro-scale characteristics of physical micro-environments, that is, soil pores, and their influence on decomposition, on CO2 emission, and on composition of bacterial communities associated with the detritus. The study consisted of a series of soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by analyses of soil pores and phylogenetic analysis of microbial communities with rRNA genes via pyrosequencing.

16S rDNA↗
DOE OSTI2024

The direct and indirect drivers shaping RNA viral communities in grassland soils

ABSTRACT Recent studies have revealed diverse RNA viral communities in soils. Yet, how environmental factors influence soil RNA viruses remains largely unknown. Here, we recovered RNA viral communities from bulk metatranscriptomes sequenced from grassland soils managed for 5 years under multiple environmental conditions including water content, plant presence, cultivar type, and soil depth. More than half of the unique RNA viral contigs (64.6%) were assigned with putative hosts. About 74.7% of these classified RNA viral contigs are known as eukaryotic RNA viruses suggesting eukaryotic RNA viruses may outnumber prokaryotic RNA viruses by nearly three times in this grassland. Of the identified eukaryotic RNA viruses and the associated eukaryotic species, the most dominant taxa were Mitoviridae with an average relative abundance of 72.4%, and their natural hosts, Fungi with an average relative abundance of 56.6%. Network analysis and structural equation modeling support that soil water content, plant presence, and type of cultivar individually demonstrate a significant positive impact on eukaryotic RNA viral richness directly as well as indirectly on eukaryotic RNA viral abundance via influencing the co-existing eukaryotic members. A significant negative influence of soil depth on soil eukaryotic richness and abundance indirectly impacts soil eukaryotic RNA viral communities. These results provide new insights into the collective influence of multiple environmental and community factors that shape soil RNA viral communities and offer a structured perspective of how RNA virus diversity and ecology respond to environmental changes. IMPORTANCE Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how environmental and community factors collectively shape soil RNA communities and contribute to ecological understanding of RNA viral survival under various environmental conditions and virus-host interactions in soil. This knowledge is critical for predicting the viral responses to climate change and the potential emergence of biothreats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

Background: Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013–2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. Results: Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. Conclusions: This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.

16S rRNA gene sequencing↗