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NASA NTRS1988

A stereo triangulation system for structural identification: Analytical and experimental results

Identification of large space structures' distributed mass, stiffness, and energy dissipation characteristics poses formidable analytical, numerical, and implementation difficulties. Development of reliable on-orbit structural identification methods is important for implementing active vibration suppression concepts which are under widespread study in the large space structures community. Near the heart of the identification problem lies the necessity of making a large number of spatially distributed measurements of the structure's vibratory response and the associated force/moment inputs with sufficient spatial and frequency resolution. In the present paper, we discuss a method whereby tens of active or passive (retro-reflecting) targets on the structure are tracked simultaneously by the focal planes of two or more video cameras mounted on an adjacent platform. Triangulation (optical ray intersection) of the conjugate image centroids yield inertial trajectories of each target on the structure. Given the triangulated motion of the targets, we apply and extend methodology developed by Creamer, Junkins, and Juang to identify the frequencies, mode shapes, and updated estimates for the mass/stiffness/damping parameterization of the structure. The methodology is semi-automated, for example, the post experiment analysis of the video imagery to determine the inertial trajectories of the targets typically requires less than thirty minutes of real time. Using methodology discussed herein, the frequency response of a large number of points on the structure (where reflective targets are mounted) on the structure can be determined from optical measurements alone. For comparison purposes, we also utilize measurements from accelerometers and a calibrated impulse hammer. While our experimental work remains in a research stage of development, we have successfully tracked and stereo triangulated 20 targets (on a vibrating cantilevered grid structure) at a sample frequency of 200 HZ, and have established conclusively the feasibility and desirability of this approach. We discuss, in summary, recent advances in analog and digital video processing methodology, actuation methods, and bring them to bear on the structural identification problem. We include a brief discussion of our experimental hardware and some recent experimental results which support the practical feasibility of this structural vibration sensing approach.

Junkins, J. L.↗

NASA NTRS2014

Locating Noctiluca Miliaris in the Arabian Sea: An Optical Proxy Approach

Coincident with shifting monsoon weather patterns over India, the phytoplankter Noctiluca miliaris has recently been observed to be dominating phytoplankton blooms in the northeastern Arabian Sea during the winter monsoons. Identifying the exact environmental and/or ecological conditions that favor this species has been hampered by the lack of concurrent environmental and biological observations on time and space scales relevant to ecologic and physiologic processes. We present a bio-optical proxy for N. miliaris measured on highly resolved depth scales coincident with hydrographic observations with the goal to identify conducive hydrographic conditions for the bloom. The proxy is derived from multichannel excitation chlorophyll a fluorescence and is validated with microscopy, pigment composition, and spectral absorption. Phytoplankton populations dominated by either diatoms or other dinoflagellates were additionally discerned. N. miliaris populations in full bloom were identified offshore in low-nutrient and low-N : P ratio surface waters within a narrow temperature and salinity range. These populations transitioned to high-biomass diatom-dominated coastal upwelling populations. A week later, the N. miliaris blooms were observed in declining phase, transitioning to very-low-biomass populations of non-N. miliaris dinoflagellates. There were no clear hydrographic conditions uniquely associated with the N. miliaris populations, although N. miliaris was not found in the upwelling or extremely oligotrophic waters. Taxonomic transitions were not discernible in the spatial structure of the bloom as identified by the ocean color Chl imagery, indicating that in situ observations may be necessary to resolve community structure, particularly for populations below the surface.

Arabian Sea↗

DOE OSTI2023

Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model

Graphene oxide (GO) nanomaterials have unique physicochemical properties that make them highly promising for biomedical, environmental, and agricultural applications. Despite the increasing interest and the use of GO, assessments of its nanotoxicity have largely not interrogated its potential impact on the gut microbiome. This study addresses an important knowledge gap by investigating the impact of GO exposure- both at low (25 ppm) and high (250ppm) doses and fed (nutrient rich) and fasted (nutrient deplete) conditions- on the gut microbial community structure and function, using an in vitro human colon bioreactor model. 16S rRNA amplicon sequencing revealed that GO exposure resulted in a restructuring of community composition. 25 ppm GO induced a marked decrease in the Bacteroidota phylum and increased the ratio of Firmicutes to Bacteroidota (F/B). Untargeted metabolomics on the supernatants indicated that 25 ppm GO impaired microbial utilization and metabolism of substrates (amino acids, carbohydrate metabolites) and reduced production of beneficial microbial metabolites such as 5-hydroxyindole-3-acetic acid and GABA. Exposure to 250 ppm GO resulted in community composition and metabolome profiles that were very similar to the controls that lacked both GO and digestive enzymes, suggesting that high concentrations of GO may interact with digestive enzymes to form protein coronas, causing their depletion in the gut environment. Differential abundance analyses revealed that 3 genera from the phylum Bacteroidota (Bacteroides, Dysgonomonas, and Parabacteroides) were more abundant after 250 ppm GO exposure, irrespective of feed state. Integrative correlation network analysis indicated that the phylum Bacteroidota showed strong positive correlations to multiple microbial metabolites including GABA and 3-indoleacetic acid, are much larger number of correlations compared to other phyla. These results show that GO exposure has a significant impact on gut microbial community composition and metabolism and different mechanisms are at play for low and high GO concentrations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Microbial abundances and carbon use under ambient temperature or experimental warming in a southern boreal peatland

Abstract Organic peat soils occupy relatively little of the global land surface area but store vast amounts of soil carbon in northern latitudes where climate is warming at a rapid pace. Warming may result in strong positive feedbacks of carbon loss and global climate change driven by microbial processes if warming alters the balance between primary productivity and decomposition. To elucidate effects of warming on the microbial communities mediating peat carbon dynamics, we explored the abundance of broad microbial groups and their source of carbon (i.e. old carbon versus more recently fixed photosynthate) using microbial lipid analysis (δ 13 C PLFA) of peat samples under ambient temperatures and before/after initiation of experimental peat warming (+ 2.25, + 4.5, + 6.75, and + 9 °C). This analysis occurred over a profile to 2 m depth in an undrained, ombrotrophic peat bog in northern Minnesota. We found that the total microbial biomass and individual indicator lipid abundances were stratified by depth and strongly correlated to temperature under ambient conditions. However, under experimental warming, statistically significant effects of temperature on the microbial community were sporadic and inconsistent. For example, 3 months after experimental warming the relative abundance of Gram-negative bacterial indicators across depth combined and > 50 cm depth and Gram-positive bacterial indicators at 20–50 cm depth showed significant positive relationships to temperature. At that same timepoint, however, the relative abundance of Actinobacterial indicators across depth showed a significant negative relationship to temperature. After 10 months of experimental warming, the relative abundance of fungal biomarkers was positively related to temperature in all depths combined, and the absolute abundance of anaerobic bacteria declined with increasing temperature in the 20–50 cm depth interval. The lack of observed response in the broader microbial community may suggest that at least initially, microbial community structure with peat depth in these peatlands is driven more by bulk density and soil water content than temperature. Alternatively, the lack of broad microbial community response may simply represent a lag period, with more change to come in the future. The long-term trajectory of microbial response to warming in this ecosystem then could either be direct, after this initial lag time, or indirect through other physical or biogeochemical changes in the peat profile. These initial results provide an important baseline against which to measure long-term microbial community and carbon-cycling responses to warming and elevated CO 2 .

Felice, Mark↗

DOE OSTI2024

Biomolecular budget of persistent, microbial-derived soil organic carbon: The importance of underexplored pools

The details of how soil microorganisms contribute to stable soil organic carbon pools are a pressing knowledge gap with direct implications for soil health and climate mitigation. It is now recognized that microbial necromass contributes substantially to the formation of stable soil carbon. However, the quantification of necromass in soils has largely been limited to model molecules such as aminosugar biomarkers. The abundance and chemical composition of other persistent microbial residues remain unresolved, particularly concerning how these pools may vary with microbial community structure, soil texture, and management practices. We use yearlong soil incubation experiments with an isotopic tracer to quantify the composition of persistent residues derived from microbial communities inhabiting sand or silt dominated soil with annual (corn) or perennial (switchgrass) monocultures. Persistent microbial residues were recovered in diverse soil biomolecular pools including metabolites, proteins, lipids, and mineral-associated organic matter (MAOM). The relative abundances of microbial contributions to necromass pools were consistent across cropping systems and soil textures. The greatest residue accumulation was not recovered in MAOM but in the light density fraction of soil debris that persisted after extraction by chemical fractionation using organic solvents. Necromass abundance was positively correlated with microbial biomass abundance and revealed a possible role of cell wall morphology in enhancing microbial carbon persistence; while gram-negative bacteria accounted for the greatest contribution to microbial-derived carbon by mass at one year, residues from gram-positive Actinobacteria and Firmicutes showed greater durability. Together these results offer a quantitative assessment of the relative importance of diverse molecular classes for generating durable soil carbon.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome

Abstract Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac -like and iad -like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad -like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad -like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures

Abstract Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis cause worldwide public and ecosystem health concerns. The response of Microcystis growth and toxin production to new and recycled nitrogen (N) inputs and the impact of heterotrophic bacteria in the Microcystis phycosphere on these processes are not well understood. Here, using microbiome transplant experiments, cyanotoxin analysis, and nanometer-scale stable isotope probing to measure N incorporation and exchange at single cell resolution, we monitored the growth, cyanotoxin production, and microbiome community structure of several Microcystis strains grown on amino acids or proteins as the sole N source. We demonstrate that the type of organic N available shaped the microbial community associated with Microcystis, and external organic N input led to decreased bacterial colonization of Microcystis colonies. Our data also suggest that certain Microcystis strains could directly uptake amino acids, but with lower rates than heterotrophic bacteria. Toxin analysis showed that biomass-specific microcystin production was not impacted by N source (i.e. nitrate, amino acids, or protein) but rather by total N availability. Single-cell isotope incorporation revealed that some bacterial communities competed with Microcystis for organic N, but other communities promoted increased N uptake by Microcystis, likely through ammonification or organic N modification. Our laboratory culture data suggest that organic N input could support Microcystis blooms and toxin production in nature, and Microcystis-associated microbial communities likely play critical roles in this process by influencing cyanobacterial succession through either decreasing (via competition) or increasing (via biotransformation) N availability, especially under inorganic N scarcity.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Microbiome assembly in thawing permafrost and its feedbacks to climate

Abstract The physical and chemical changes that accompany permafrost thaw directly influence the microbial communities that mediate the decomposition of formerly frozen organic matter, leading to uncertainty in permafrost–climate feedbacks. Although changes to microbial metabolism and community structure are documented following thaw, the generality of post‐thaw assembly patterns across permafrost soils of the world remains uncertain, limiting our ability to predict biogeochemistry and microbial community responses to climate change. Based on our review of the Arctic microbiome, permafrost microbiology, and community ecology, we propose that Assembly Theory provides a framework to better understand thaw‐mediated microbiome changes and the implications for community function and climate feedbacks. This framework posits that the prevalence of deterministic or stochastic processes indicates whether the community is well‐suited to thrive in changing environmental conditions. We predict that on a short timescale and following high‐disturbance thaw (e.g., thermokarst), stochasticity dominates post‐thaw microbiome assembly, suggesting that functional predictions will be aided by detailed information about the microbiome. At a longer timescale and lower‐intensity disturbance (e.g., active layer deepening), deterministic processes likely dominate, making environmental parameters sufficient for predicting function. We propose that the contribution of stochastic and deterministic processes to post‐thaw microbiome assembly depends on the characteristics of the thaw disturbance, as well as characteristics of the microbial community, such as the ecological and phylogenetic breadth of functional guilds, their functional redundancy, and biotic interactions. These propagate across space and time, potentially providing a means for predicting the microbial forcing of greenhouse gas feedbacks to global climate change.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Beyond the usual suspects: methanogenic communities in eastern North American peatlands are also influenced by nickel and copper concentrations

Peatlands both accumulate carbon and release methane, but their broad range in environmental conditions means that the diversity of microorganisms responsible for carbon cycling is still uncertain. Here, we describe a community analysis of methanogenic archaea responsible for methane production in 17 peatlands from 36 to 53 N latitude across the eastern half of North America, including three metal-contaminated sites. Methanogenic community structure was analysed through Illumina amplicon sequencing of the mcrA gene. Whether metal-contaminated sites were included or not, metal concentrations in peat were a primary driver of methanogenic community composition, particularly nickel, a trace element required in the F 430 cofactor in methyl-coenzyme M reductase that is also toxic at high concentrations. Copper was also a strong predictor, likely due to inhibition at toxic levels and/or to cooccurrence with nickel, since copper enzymes are not known to be present in anaerobic archaea. Here, the methanogenic groups Methanocellales and Methanosarcinales were prevalent in peatlands with low nickel concentrations, while Methanomicrobiales and Methanomassiliicoccales were abundant in peatlands with higher nickel concentrations. Results suggest that peat-associated trace metals are predictors of methanogenic communities in peatlands.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Prescribed fire selects for a pyrophilous soil sub‐community in a northern California mixed conifer forest

Abstract Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above‐ground response to fire has been well‐documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. To understand how soil microbial communities respond to prescribed fire, we sampled four plots at a high temporal resolution (two burned, two controls), for 17 months, in a mixed conifer forest in northern California, USA. Using amplicon sequencing, we found that prescribed fire significantly altered both fungal and bacterial community structure. We found that most differentially abundant fungal taxa had a positive fold‐change, while differentially abundant bacterial taxa generally had a negative fold‐change. We tested the null hypothesis that these communities assembled due to neutral processes (i.e., drift and/or dispersal), finding that >90% of taxa fit this neutral prediction. However, a dynamic sub‐community composed of burn‐associated indicator taxa that were positively differentially abundant was enriched for non‐neutral amplicon sequence variants, suggesting assembly via deterministic processes. In synthesizing these results, we identified 15 pyrophilous taxa with a significant and positive response to prescribed burns. Together, these results lay the foundation for building a process‐driven understanding of microbial community assembly in the context of the classical disturbance regime of fire.

Microbiology↗

DOE OSTI2022

Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Abstract Background Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities. Results To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum ( Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted sorghum-degrading communities, including Actinotalea , Filomicrobium , and Gemmatimonadetes populations. Functional analysis demonstrated that the microbiomes proceeded through successive stages that are linked to enzymes that deconstruct plant cell wall polymers. The combination of network and functional analysis highlighted the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes. Conclusions The two-tier cultivation of compost-derived microbiomes on sorghum led to the establishment of microbiomes for which community structure and performance could be assessed. The work reinforces the observation that subtle differences in community composition and the genomic content of strains may lead to significant differences in community performance.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A framework for soil microbial ecology in urban ecosystems

Nearly all ecosystems host diverse microbiomes that support vital ecosystem processes. At the same time, these ecosystems and their microbiomes are increasingly altered by human activities, particularly in highly managed urban environments. While microbial ecologists are beginning to understand the drivers of microbial assembly and the link between community structure and function in many ecosystems, few of these advances have been applied to urban ecosystems. In this synthesis, we review research on the urban soil microbiome and develop a framework to integrate soil microbial communities with urban ecosystem function. We identify disturbance, altered resources, and heterogeneity as key drivers through which human activities including urban development affect soils and their resident microorganisms. Steep environmental gradients in many urban systems present a unique opportunity to address fundamental questions in microbial ecology, such as how microbes respond to stress and how biogeochemical rates relate to microbial diversity and composition. Soil microbiomes in cities also provide ecosystem services and harms, making it crucial to understand how human activity drives those functions and the consequences for environmental and human health. We argue that much-needed integration across disturbance ecology, urban ecology, and microbial ecology will help generate practical and equitable strategies for managing ecosystem benefits in cities where most humans now live.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands

Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of salt-water intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. In conclusion, these changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates

Miscanthus × giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands; however, the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S small subunit (SSU) rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA or RNA. Similar numbers of membership were detected in DNA and RNA microbial communities, with more than 90% of membership shared. However, the profile of dominant membership within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-fold higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient

In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO43-). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO43- from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO₄³⁻ and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO₄³-. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.

arbuscular mycorrhizal fungi↗

DOE OSTI2024

Climate, food and humans predict communities of mammals in the United States

Abstract Aim The assembly of species into communities and ecoregions is the result of interacting factors that affect plant and animal distribution and abundance at biogeographic scales. Here, we empirically derive ecoregions for mammals to test whether human disturbance has become more important than climate and habitat resources in structuring communities. Location Conterminous United States. Time Period 2010–2021. Major Taxa Studied Twenty‐five species of mammals. Methods We analysed data from 25 mammal species recorded by camera traps at 6645 locations across the conterminous United States in a joint modelling framework to estimate relative abundance of each species. We then used a clustering analysis to describe 8 broad and 16 narrow mammal communities. Results Climate was the most important predictor of mammal abundance overall, while human population density and agriculture were less important, with mixed effects across species. Seed production by forests also predicted mammal abundance, especially hard‐mast tree species. The mammal community maps are similar to those of plants, with an east–west split driven by different dominant species of deer and squirrels. Communities vary along gradients of temperature in the east and precipitation in the west. Most fine‐scale mammal community boundaries aligned with established plant ecoregions and were distinguished by the presence of regional specialists or shifts in relative abundance of widespread species. Maps of potential ecosystem services provided by these communities suggest high herbivory in the Rocky Mountains and eastern forests, high invertebrate predation in the subtropical south and greater predation pressure on large vertebrates in the west. Main Conclusions Our results highlight the importance of climate to modern mammals and suggest that climate change will have strong impacts on these communities. Our new empirical approach to recognizing ecoregions has potential to be applied to expanded communities of mammals or other taxa.

Kays, Roland↗

DOE OSTI2024

Genomic insights into redox-driven microbial processes for carbon decomposition in thawing Arctic soils and permafrost

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Organic matter distribution in the icy environments of Taylor Valley, Antarctica

Glaciers can accumulate and release organic matter affecting the structure and function of associated terrestrial and aquatic ecosystems. Here we analyzed 18 ice cores collected from six locations in Taylor Valley (McMurdo Dry Valleys), Antarctica to determine the spatial abundance and quality of organic matter, and the spatial distribution of bacterial density and community structure from the terminus of the Taylor Glacier to the coast (McMurdo Sound). Our results showed that dissolved and particulate organic carbon (DOC and POC) concentrations in the ice core samples increased from the Taylor Glacier to McMurdo Sound, a pattern also shown by bacterial cell density. Fluorescence Excitation Emission Matrices Spectroscopy (EEMs) and multivariate parallel factor (PARAFAC) modeling identified one humic-like (C1) and one protein-like (C2) component in ice cores whose fluorescent intensities all increased from the Polar Plateau to the coast. The fluorescence index showed that the bioavailability of dissolved organic matter (DOM) also decreased from the Polar Plateau to the coast. Partial least squares path modeling analysis revealed that bacterial abundance was the main positive biotic factor influencing both the quantity and quality of organic matter. Marine aerosol influenced the spatial distribution of DOC more than katabatic winds in the ice cores. Certain bacterial taxa showed significant correlations with DOC and POC concentrations. Collectively, our results show the tight connectivity among organic matter spatial distribution, bacterial abundance and meteorology in the McMurdo Dry Valley ecosystem.

54 ENVIRONMENTAL SCIENCES↗