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DOE OSTI2024

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRSDate not supplied

Responses of Microbes to Modeled Space Radiation

The built environment of spaceships is host to a microbial community that affects crew and craft alike. While the static composition of this community has been characterized and its temporal dynamics examined, the mechanisms controlling its make-up and evolutionary trajectory are not understood. Systematic analyses of microbial diversity show consistent patterns in community composition and function. Understanding these patterns' ecological origins remains a significant challenge, as it requires connecting processes at varying temporal and spatial scales. However, it is clear that the state and trajectories of microbial communities are in-part determined by their physical environment. In this regard, the spaceflight environment includes numerous interacting factors that differentiate it from Earth environments, including an altered atmospheric composition, reduced gravity (and thus altered fluid dynamics), and increased ionizing radiation. These factors impart selective pressures on microbial communities that affect their evolutionary trajectories and thus the risks and benefits these communities represent to crew and craft. The radiation environment of space leads to chronic exposure to low doses and is difficult to mimic on Earth. Thus, little is known about how microbial communities in spacecraft will respond and evolve. Therefore, given the limitations of existing studies, we aim to empirically determine how exposure to low doses of ionizing radiation for thousands of cell divisions affects rates of mutation accumulation in bacteria and the trajectory of their evolution. In this way, we will provide a critical set of data for designing safe and robust space missions. Here we discuss our progress towards this aim, including the construction of exposure facilities, our culturing and analysis approach, and preliminary data.

radiation↗

DOE OSTI2025

Diverging drivers of fungal diversity: seasonal effects shape aboveground communities, while geographical patterns govern belowground communities in rubber tree ecosystems

Understanding the spatiotemporal dynamics of microbial communities is essential for predicting their ecological roles and interactions with host plants. In a recent study, Wei and colleagues (Microbiol Spectr 13:e02097-24, 2024) investigated fungal diversity across multiple plant and soil compartments in rubber trees over two seasons and two geographically distinct regions in China. Their findings revealed that alpha diversity was primarily influenced by seasonal changes and physicochemical factors, while beta diversity exhibited a strong geographical pattern, shaped by leaf phosphorus and soil available potassium. These results highlight the role of environmental drivers in shaping within-community diversity, while other factors contribute to the differences between fungal communities across the soil–plant continuum. By distinguishing the effects of temporal and spatial factors, this study provides detailed insights into plant-associated microbiomes and emphasizes the need for further research on the functional implications of microbial diversity in the context of changing environmental and agricultural conditions.

fungal diversity↗

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

Bootstrapping outperforms community‐weighted approaches for estimating the shapes of phenotypic distributions

Abstract Estimating phenotypic distributions of populations and communities is central to many questions in ecology and evolution. These distributions can be characterized by their moments (mean, variance, skewness and kurtosis) or diversity metrics (e.g. functional richness). Typically, such moments and metrics are calculated using community‐weighted approaches (e.g. abundance‐weighted mean). We propose an alternative bootstrapping approach that allows flexibility in trait sampling and explicit incorporation of intraspecific variation, and show that this approach significantly improves estimation while allowing us to quantify uncertainty. We assess the performance of different approaches for estimating the moments of trait distributions across various sampling scenarios, taxa and datasets by comparing estimates derived from simulated samples with the true values calculated from full datasets. Simulations differ in sampling intensity (individuals per species), sampling biases (abundance, size), trait data source (local vs. global) and estimation method (two types of community‐weighting, two types of bootstrapping). We introduce the traitstrap R package, which contains a modular and extensible set of bootstrapping and weighted‐averaging functions that use community composition and trait data to estimate the moments of community trait distributions with their uncertainty. Importantly, the first function in the workflow, trait_fill , allows the user to specify hierarchical structures (e.g. plot within site, experiment vs. control, species within genus) to assign trait values to each taxon in each community sample. Across all taxa, simulations and metrics, bootstrapping approaches were more accurate and less biased than community‐weighted approaches. With bootstrapping, a sample size of 9 or more measurements per species per trait generally included the true mean within the 95% CI. It reduced average percent errors by 26%–74% relative to community‐weighting. Random sampling across all species outperformed both size‐ and abundance‐biased sampling. Our results suggest randomly sampling ~9 individuals per sampling unit and species, covering all species in the community and analysing the data using nonparametric bootstrapping generally enable reliable inference on trait distributions, including the central moments, of communities. By providing better estimates of community trait distributions, bootstrapping approaches can improve our ability to link traits to both the processes that generate them and their effects on ecosystems.

Maitner, Brian S.↗

DOE OSTI2022

Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2022

Adaptation to environmental extremes structures functional traits in biological soil crust and hypolithic microbial communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semi-translucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities waging war using the Type VI Secretion System (T6SS) and hypoliths favoring diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems.

Biological soil crusts↗

DOE OSTI2022

Does mycorrhizal symbiosis determine the climate niche for Populus as a bioenergy feedstock?

This is the final technical and scientific report for DE-SC0016097, in which we investigated the role of symbiotic fungi in determining the climatic niche of trees. While microbes have long been viewed as agents of disease, recent explorations of the microbiome have led biologists to recognize that beneficial microbes play an equally vital role in maintaining the health of plants and animals. Perhaps the most ubiquitous form of beneficial interaction in terrestrial ecosystems occurs between fungi and plant roots. These fungus-root, or “mycorrhizal”, symbioses involve the reciprocal exchange of plant sugars for soil nutrients obtained by the fungus, such as nitrogen and phosphorous, which are critical for plant growth. It is known that mycorrhizal associations are widespread - occurring in approximately 90% of plant species - and diverse, with single plants able to associate simultaneously with over 100 species of fungi. Despite this, the ecological factors that control large-scale distribution and abundance of mycorrhizal symbioses are still poorly known, making it challenging to predict how mycorrhizal symbioses may change in future climate conditions or how these fungal communities might be manipulated to improve regional agriculture or forestry projects. In this research project we focused on a native North American tree with strong biofuel potential – Populus – to answer fundamental questions about the role of climate, soil environment, and mycorrhizal interactions in determining growth and competition in plant communities. Populus provides a unique opportunity for ecologically relevant experiments because of its widespread distribution across North America and its natural variability in mycorrhizal association types.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Trait relationships of fungal decomposers in response to drought using a dual field and laboratory approach

Abstract Decomposer fungi play a fundamental role in terrestrial ecosystem dynamics. In the southwestern United States, climate change is causing more frequent and severe droughts, which may alter fungal community composition and activity. Investigating relationships between fungal traits may improve the prediction of fungal responses to drought. In this dual field and laboratory experiment, we examine whether trade‐offs occur between traits associated with drought. Specifically, we test the hypothesis that fungi sort into lifestyles specializing in growth y ield, resource a cquisition, and drought s tress tolerance (“YAS” framework). For the field experiment, we constructed microbial “cages” containing sterilized litter and 1 of 10 fungal isolates. These cages were placed in long‐term drought and control plots in a southern Californian grassland for 6 and 12 months. We measured fungal hyphal length per unit litter mass loss for growth yield, the potential activities of four extracellular enzymes for resource acquisition, and the ability to grow in the drought versus control plots for drought stress tolerance. We compared these results with a laboratory microcosm experiment constructed with the same fungal isolates and that measured the same fungal traits. The field experiment corroborated our laboratory results, in that no trade‐offs were observed between growth yield and resource acquisition traits. However, in contrast to the laboratory experiment, drought tolerance was negatively related to extracellular enzyme activity and growth yield in the field, implying a trade‐off. Despite this observed trade‐off in the field, growth yield was not hindered by drought. We propose a modification to the YAS framework, by combining the growth yield and resource acquisition lifestyles, which may be more appropriate for this arid system. This joint laboratory and field approach contextualizes a theoretical framework in microbial ecology and improves understanding of fungal community response to climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

A reporting format for field measurements of soil respiration

Field observations of the soil-to-atmosphere CO2 flux–soil respiration, RS–are a prime example of ‘long tail’ data that historically have had neither centralized databases nor an agreed-upon reporting format. This has hindered scientific transparency, analytical reproducibility, and novel syntheses with respect to this globally-important component of the carbon cycle. Here we propose a new data and metadata reporting format for RS data, based on engagement with a wide range of researchers in the field as well as expert advisory panels. Our goal was a reporting format that would be relevant and useful for synthesis activities, and optimizing data discoverability and usability while not placing an undue burden on data contributors. We describe previous RS data collection efforts, lessons learned from related databases and data-oriented networks (e.g. FLUXNET) in earth and ecological sciences, and the process of community consultation. The proposed reporting format focuses on chamber-level data and metadata, specifying measurement conditions and, for a given measurement period defined by beginning and ending timestamps, a mean RS flux (or CO2 concentration) and associated ancillary measurements. Fundamentally, this format aims to enable findable, accessible, interoperable, and reusable data, while providing ‘future-proofing’ capabilities to support reanalyses using as yet unknown algorithms or approaches. Finally, this proposed RS reporting format is available online, and is intended to be a dynamic document, subject to further community feedback and/or change in the future.

Bond-Lamberty, Benjamin↗

DOE OSTI2023

IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Central Hanford Ecological Integrity Assessments: Final Report

The Hanford Site is comprised of an expanse of shrub-steppe habitats that provides exceptional ecological value to plants and animals located on the site and in the surrounding greater Columbia Basin. The U.S. Department of Energy, Hanford Field Office (HFO)-managed portion of the Hanford Site, referred to herein as Central Hanford, has been the focus of various ecological monitoring efforts, such as vegetation monitoring. The scope and goals of vegetation surveys have varied greatly since the Hanford Site was established, but studies have documented a rapidly changing landscape, making it clear that routine vegetation monitoring is integral to understanding ecological changes and preserving the ecological value of the Hanford Site. A new vegetation monitoring effort was initiated in calendar year (CY) 2023 and continued through CY 2025 using methods based on ecological integrity assessments (EIA) (NHR-2024-04, Field Manual for Applying Rapid Ecological Integrity Assessments in Upland Plant Communities of Washington State ) developed by the Washington Natural Heritage Program (WNHP), a division of the Department of Natural Resources (DNR), and NatureServe.® The methods were modified and supplemented to meet monitoring goals at the Hanford Site. The EIA monitoring effort consisted of field surveys to evaluate vegetation and soil conditions for upland habitats throughout Central Hanford. Vegetation cover estimates were used to score a variety of metrics for vegetation condition. This report summarizes monitoring methods, monitoring results, and provides management recommendations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Editorial: Subsurface microbiology within hydrocarbon resources or stored gases

A Research Topic on the microbiology of hydrocarbon and gas storage reservoirs has far reaching industrial applications. In recent decades, there has been a growing interest in understanding microbial communities in subsurface energy reservoirs, such as coal, oil, and shale beds. This area of research has broadened to include gas storage reservoirs for hydrogen and CO 2 . Scientists are beginning to unravel the unexpected impact microorganisms have on these systems, through changing the fluid geochemistry, the gas content, and even the permeability. By recognizing the influence of these tiny organisms on our engineered environments, we can develop better risk assessments, target mitigation strategies, expand energy production, and refine operational guidance, ultimately contributing to a more sustainable energy future.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1973

Multispectral scanner imagery for plant community classification.

Optimum channel selection among 12 channels of multispectral scanner imagery identified six as providing the best information for computerized classification of 11 plant communities and two nonvegetation classes. Intensive preprocessing of the spectral data was required to eliminate bidirectional reflectance effects of the spectral imagery caused by scanner view angle and varying geometry of the plant canopy. Generalized plant community types - forest, grassland, and hydrophytic systems - were acceptably classified based on ecological analysis. Serious, but soluble, errors occurred with attempts to classify specific community types within the grassland system. However, special clustering analyses provided for improved classification of specific grassland communities.

Driscoll, R. S.↗

NASA NTRS1991

Communications infrastructure requirements for telemedicine/telehealth in the context of planning for and responding to natural disasters: Considering the need for shared regional networks

During the course of recent years the frequency and magnitude of major disasters - of natural, technological, or ecological origin - have made the world community dramatically aware of the immense losses of human life and economic resources that are caused regularly by such calamities. Particularly hard hit are developing countries, for whom the magnitude of disasters frequently outstrips the ability of the society to cope with them. In many cases this situation can be prevented, and the recent trend in disaster management has been to emphasize the importance of preparedness and mitigation as a means of prevention. In cases of disaster, a system is needed to respond to relief requirements, particularly the delivery of medical care. There is no generic telecommunications infrastructure appropriate for the variety of applications in medical care and disaster management. The need to integrate telemedicine/telehealth into shared regional disaster management telecommunications networks is discussed. Focus is on the development of infrastructure designed to serve the needs of disaster prone regions of the developing world.

Scott, John Carver↗

NASA NTRS1995

Validating spatial structure in canopy water content using geostatistics

Heterogeneity in ecological phenomena are scale dependent and affect the hierarchical structure of image data. AVIRIS pixels average reflectance produced by complex absorption and scattering interactions between biogeochemical composition, canopy architecture, view and illumination angles, species distributions, and plant cover as well as other factors. These scales affect validation of pixel reflectance, typically performed by relating pixel spectra to ground measurements acquired at scales of 1m(exp 2) or less (e.g., field spectra, foilage and soil samples, etc.). As image analysis becomes more sophisticated, such as those for detection of canopy chemistry, better validation becomes a critical problem. This paper presents a methodology for bridging between point measurements and pixels using geostatistics. Geostatistics have been extensively used in geological or hydrogeolocial studies but have received little application in ecological studies. The key criteria for kriging estimation is that the phenomena varies in space and that an underlying controlling process produces spatial correlation between the measured data points. Ecological variation meets this requirement because communities vary along environmental gradients like soil moisture, nutrient availability, or topography.

Sanderson, E. W.↗

NASA NTRS2002

Biogeochemistry of Microbial Mats

The hierarchical organization of microbial ecosystems determines the rates of processes that shape Earth's environment, define the stage upon which major evolutionary events occurred, and create biosignatures in sediments and atmospheres. In cyanobacterial mats, oxygenic photosynthesis provides energy, organic substrates and oxygen to the ecosystem. Incident light changes with depth in the mat, both in intensity and spectral composition, and counteracting gradients of oxygen and sulfide shape the chemical microenvironment. A combination of benefits and hazards of light, oxygen and sulfide promotes the allocation of the various essential mat processes between light and dark periods and to various depths in the mat. Microliters produce hydrogen, small organic acids, nitrogen and sulfur species. Such compounds fuel a flow of energy and electrons in these ecosystems and thus shape interactions between groups of microorganisms. Coordinated observations of population distribution, abundance, and activity for an entire community are making fundamental questions in ecology accessible. These questions address those factors that sustain the remarkable diversity of microorganisms that are now being revealed by molecular techniques. These questions also target the processes that shape the various kinds of biosignatures that we will seek, both in ancient rocks from Earth and Mars, and in atmospheres of distant planets beyond our Solar System.

DesMarais, David J.↗