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NASA NTRS2020

Global Data Assembly Center (gdac) Report to the GHRSST Science Team

In 2019-2020 the Global Data Assembly Center (GDAC) at NASA’s Physical Oceanography Distributed Active Archive Center (PO.DAAC) provided ingest, archive, distribution and user services for GHRSST operational data streams with improved and evolved tools, services, and tutorials, and interfaced with the user community to address technical inquiries. Several new GHRSST datasets including reprocessed MODIS Aqua/Terra L2P with improved cloud screening were made available. The PO.DAAC participated in the evolving GHRSST data management re architecture and development activities. GHRSST Science Team member Edward Armstrong assumed the role of co-leader of the CEOS SST Virtual Constellation. The following sections summarize and document the specific achievements of the GDAC to the GHRSST community.

Finch, Chris↗
DOE OSTI2025

A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse

Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.

Kordia↗
DOE OSTI2024

DOE BSSD Performance Management Metrics Report Q1

Microbes play key roles in our biosphere, from driving global nutrient cycling to impacting plant, animal and human health and disease. Complex data from microbial genomes, proteins, and metabolites provide a window into these tiny engines that drive life on our planet. Yet these data are dispersed among researchers’ laboratories and various repositories, making it difficult to access. This calls for new ways of managing data, improving data interoperability, advancing community standards, and creating an infrastructure where data are shared efficiently. We have built the National Microbiome Data Collaborative (NMDC) to advance how scientists create, use, and reuse data to redefine the way we understand and harness the power of microbes. The vision of the National Microbiome Data Collaborative (NMDC) is to drive a microbiome data sharing network connecting data, people, and ideas to advance microbiome innovation and discovery. The NMDC was launched in 2019 and brought together DOE National Laboratories to collaborate across resources, capabilities, and expertise. The NMDC team was strategically assembled to include software developers, microbial researchers, metadata experts, and multi-omics specialists. The diversity of the NMDC team reflects the inherently interdisciplinary nature of microbiome science, and we leverage the strengths of the DOE National Laboratory system. Towards BER’s goal of advancing an iterative systems biology approach to the understanding of microbial genomes, the NMDC serves as a foundation for infrastructure, data standards, and community building. Together with the flagship DOE User Facilities, the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), we are developing core capabilities in metadata standards for environmental descriptors and sample handling and processing; standardized bioinformatic workflows; an interface for data search and access; and robust community engagement activities. The NMDC production platform supports long-term data infrastructure and community building for BER’s bioenergy and environmental research goals. Our approach leverages lessons learned and an ambitious framework for collaborative, interdisciplinary data infrastructure to support microbiome research. The NMDC supports data, information, and knowledge access through three defined software tools – the Submission Portal, NMDC EDGE, and the Data Portal – driven by community needs. Herein, we describe the value proposition for the microbiome research community, our overarching strategy, and challenges and opportunities for developing the NMDC as both an infrastructure and community engagement program.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metagenomic and Metatranscriptomic Analyses Revealed Uncultured Bacteroidales Populations as the Dominant Proteolytic Amino Acid Degraders in Anaerobic Digesters

Current understanding of amino acid (AA) degraders in anaerobic digesters is mainly based on cultured species, whereas microorganisms that play important roles in a complex microbial community remain poorly characterized. This study investigated short-term enrichments degrading single AAs using metagenomics and metatranscriptomics. Metagenomic analysis revealed that populations related to cultured AA degraders had an abundance <2.5% of the sequences. In contrast, metagenomic-assembled bins related to uncultured Bacteroidales collectively accounted for >35% of the sequences. Phylogenetic analyses suggested that these Bacteroidales populations represented a yet-to-be characterized family lineage, i.e., Bacteroidetes vadinHA17. The bins possessed the genetic capacity related to protein degradation, including surface adhesion (3–7 genes), secreted peptidase (52–77 genes), and polypeptide-specific transporters (2–5 genes). Furthermore, metatranscriptomics revealed that these Bacteroidales populations expressed the complete metabolic pathways for degrading 16 to 17 types of AAs in enrichments fed with respective substrates. These characteristics were distinct from cultured AA degraders including Acidaminobacter and Peptoclostridium, suggesting the uncultured Bacteroidales were the major protein-hydrolyzing and AA-degrading populations. These uncultured Bacteroidales were further found to be dominant and active in full-scale anaerobic digesters, indicating their important ecological roles in the native habitats. “Candidatus Aminobacteroidaceae” was proposed to represent the previously uncharted family Bacteroidetes vadinHA17.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress

Background The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress. Results Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that anti- viral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities. Conclusions Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually updated as new genes are discovered.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

An updated LLVM-based quantum research compiler with further OpenQASM support

Abstract Quantum computing is a rapidly growing field with the potential to change how we solve previously intractable problems. Emerging hardware is approaching a complexity that requires increasingly sophisticated programming and control. Scaffold is an older quantum programming language that was originally designed for resource estimation for far-future, large quantum machines, and ScaffCC is the corresponding LLVM-based compiler. For the first time, we provide a full and complete overview of the language itself, the compiler as well as its pass structure. While previous works Abhari et al (2015 Parallel Comput. 45 2–17), Abhari et al (2012 Scaffold: quantum programming language https://cs.princeton.edu/research/techreps/TR-934-12 ), have piecemeal descriptions of different portions of this toolchain, we provide a more full and complete description in this paper. We also introduce updates to ScaffCC including conditional measurement and multidimensional qubit arrays designed to keep in step with modern quantum assembly languages, as well as an alternate toolchain targeted at maintaining correctness and low resource count for noisy-intermediate scale quantum (NISQ) machines, and compatibility with current versions of LLVM and Clang. Our goal is to provide the research community with a functional LLVM framework for quantum program analysis, optimization, and generation of executable code.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Development and Porting of Nuclear Reactor Computational Models for the NRIC Virtual Test Bed in FY23

The U.S. DOE’s National Reactor Innovation Center (NRIC) hosts an open-source website and associated GitHub repository called the Virtual Test Bed (VTB) on which computational models for advanced reactors are documented and shared with the reactor community. In FY23 under the NRIC program, computational models for nuclear reactor analysis were developed and contributed to the VTB Github repository during FY23 by contributors at Argonne National Laboratory. Other models developed outside of NRIC were also ported to the VTB as part of this work, serving a broader mission to make computational reactor analysis models more widely available to the reactor community. The model development activities focused on demonstration of gas-cooled microreactor models including computational fluid dynamics simulations of flow through an industry-inspired air jacket design, and simulation of multiphysics transients for a gas-cooled microreactor assembly. Additionally, development of a molten salt reactor (led at Idaho National Laboratory) was supported through Argonne’s expertise in multigroup cross sections generation. Models for these two reactor types were targeted due to their relevancy to NRIC’s Demonstration of Microreactor Experiments (DOME) and Laboratory for Operation and Testing in the U.S. (LOTUS) physical test beds, which are slated to host microreactor and molten salt reactor experiments. The model porting activities consisted of developing detailed documentation for several physics models which originate from the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. We include only contributions from Argonne National Laboratory in this report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRS2023

The Assembly, Test, and Integration of LOFTID (Low-Earth Orbit Flight Test of an Inflatable Decelera-tor)

R.J. Bodkin Biography Mr. Bodkin worked in industry for a rapid prototype company focusing on UAVs and manned experimental aircraft. Later he served as the Inflation System Lead on IRVE-II and 3 and the Re-Entry Vehicle Lead for LOFTID at NASA Langley Research Center. Introduction: The Low-Earth Orbit Flight Test of an Inflatable Decelerator (LOFTID), developed in partnership with United Launch Alliance (ULA) and flown in conjunction with the National Oceanic and Atmospheric Administration (NOAA) Joint Polar Satellite System-2 (JPSS-2) satellite, demonstrated Hypersonic Inflatable Aerodynamic Decelerator (HIAD) technology has progressed and is ready for mission infusion. LOFTID’s success demonstrates that aeroshells are not limited to the internal diame-ter of the launch vehicle payload fairing, allowing larger payloads to be deployed to the surfaces of planetary bodies with atmospheres. The challenges of assembling, integrating, and testing this revolutionary spacecraft will be dis-cussed as well as issues associated with doing this with a fixed launch date the project did not control. Assembly: Because LOFTID flew as a rideshare partner with JPSS-2, it was constrained with addi-tional schedule, milestone, and technical require-ments that were beyond the project’s control. As-sembly of the LOFTID hardware was challenged with the normal mechanical fit issues while also having to navigate the SARS-COVID-II pandemic. Challenges ranged from availability of team per-sonnel required on-site for vehicle assembly to dif-ficulties associated with team collaboration while working remotely and increased costs and lead times of components due to supply chain con-straints. Numerous additional challenges cascaded from the additional time required. Integration: LOFTID flew as a secondary pay-load to JPSS-2 in a mission-unique configuration, directly under JPSS-2 primary payload, inside the Payload Adapter that integrated JPSS-2 to the Atlas V launch vehicle. A mission unique Payload Adapt-er Separation System (PASS) was required to sepa-rate the Payload Adapter from the Launch Vehicle prior to the start of the LOFTID flight demonstra-tion. Development of this system was challenging due to a shortened development schedule resulting from the iterative nature of Payload Adapter devel-opment with the partners at ULA. Preparations to integrate the main segments of the LOFTID vehicle posed unique challenges of having to accommodate issues with a fixed launch date that led to some cre-ative solutions to the integration. The partnership agreement with ULA and JPSS-2 resulted in a mass simulator designed to be installed late in the inte-gration in the event the LOFTID vehicle was not ready in time.. Test: LOFTID testing was carried out in several phases. Some components were tested at the com-ponent level, others at the sub-system levels and then finally the integrated vehicle level. This culmi-nated with the Complete Systems Test (CST) per-formed in a vacuum chamber as one of the final checkouts prior to disassembly for re-packing of the aeroshell. CST challenges will be discussed as well as obstacles encountered post-CST. After CST, the vehicle was disassembled so the HIAD could be repacked, and the vehicle was reassembled for ac-ceptance vibration testing. Testing concluded with the fully assembled vehicle being shipped to the launch site for final testing and integrations with the Payload Adapter to JPSS-2 for launch and opera-tions. Conclusion: The challenges posed by the AI&T for LOFTID could inform the planetary community of some of the opportunities and challenges of de-veloping technologies on a rideshare with a rela-tively small budget.

R.J. Bodkin↗
DOE OSTI2025

The Elements of Life, Photosynthesis and Genomics

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute’s efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation, and large transcriptomic and proteomic datasets — focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors — that are well-used and appreciated by the community. Finally, a new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true “green yeast” and as a platform for engineering algae to produce useful bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1977

Telemedicine: An expanding new science on land and sea

Several medical and technical men in San Diego County are concerned with the need in many rural communities for a 24-hour day, 7-days a week access to adequate medical care. People isolated from urban areas by travel-times of 40-minutes tend to delay seeking early and effective medical care. The authors were able to assemble quality technology which permits narrow-band video-pictures, better known in the CB trade as ROBOT slow-scan television (SSTV), to be transmitted over telephone lines, by micro-wave, through satellite-bounce, or by HF-radio. These 'ROBOT' pictures can be accompanied with explanatory audio communication and with diagnostic signals from electronic instruments.

Jackman, K. R.↗
NASA NTRS2006

A Year in the Life of International Space Station

The past twelve months (October 2005 to September 2006) have been among the busiest in the life of the International Space Station (ISS), both in terms of on-orbit operations as well as future planning, for both ISS systems and research. The Expedition 12 and 13 crews completed their missions successfully, carrying out research for Russia, the United States, Europe and Japan, and bringing continuous ISS occupancy to nearly six years. The European Space Agency's (ESA) first Long Duration Mission on ISS is underway, involving significant international research. The Expedition 14 crew completed its training and is embarking on its own 6-month mission with a full slate of international research. Future crews are in training for their respective assembly and research missions. Shuttle flights resumed after a 10-month hiatus, delivering new research facilities and resuming assembly of ISS. ESA's Columbus research module was delivered to the Kennedy Space Center, joining Japan's Kibo research module already there. Following preflight testing, the two modules will launch in 2007 and 2008, respectively, joining Destiny as ISS's research infrastructure. A revised ISS configuration and assembly sequence were endorsed by all the Partners, with a reduced number of Shuttle flights, but for the first time including plans for post-Shuttle ISS operations after 2010. The new plan will pose significant challenges to the ISS research community. As Europe and Japan build their on-orbit research infrastructure, and long-term plans become firmer, the next 12 months should prove to be equally challenging and exciting.

Uri, John J.↗
NASA NTRS2006

Data Integration Support for Data Served in the OPeNDAP and OGC Environments

NASA is coordinating a technology development project to construct a gateway between system components built upon the Open-source Project for a Network Data AcceSs Protocol (OPeNDAP) and those made available made available via interfaces specified by the Open Geospatial Consortium (OGC). This project is funded though the Advanced Collaborative Connections for Earth-Sun System Science (ACCESS) Program and is a NASA contribution to the Committee on Earth Satellites (CEOS) Working Group on Information Systems and Services (WGISS). The motivation for the project is the set of data integration needs that have been expressed by the Coordinated Enhanced Observing Period (CEOP), an international program that is addressing the study of the global water cycle. CEOP is assembling a large collection in situ and satellite data and mode1 results from a wide variety of sources covering 35 sites around the globe. The data are provided by systems based on either the OPeNDAP or OGC protocols but the research community desires access to the full range of data and associated services from a single client. This presentation will discuss the current status of the OPeNDAP/OGC Gateway Project. The project is building upon an early prototype that illustrated the feasibility of such a gateway and which was demonstrated to the CEOP science community. In its first year as an ACCESS project, the effort has been has focused on the design of the catalog and data services that will be provided by the gateway and the mappings between the metadata and services provided in the two environments.

McDonald, Kenneth R.↗
NASA NTRS2014

NASA-DoD Lower Process Temperature Lead-Free Solder Project Overview

This project is a follow-on effort to the Joint Council on Aging AircraftJoint Group on Pollution Prevention (JCAAJG-PP) Pb-free Solder Project and NASA-DoD Lead-Free Electronics Project which were the first projects to test the reliability of Pb-free solder joints against the requirements of the aerospace and military community. This effort would continue to build on the results from the JCAAJG-PP Lead-Free Solder Project and NASA-DoD Lead-Free Electronics Project while focusing on a particular failure mechanism currently plaguing Pb-free assemblies, pad cratering.The NASA-DoD Lead-Free Electronics Project confirmed that pad cratering is one of the dominant failure modes that occur in various board level reliability tests, especially under dynamic loading. Pad Cratering is a latent defect that may occur during assembly, rework, and post assembly handling and testing.

electronics↗
DOE OSTI2026

Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer

The degradation of organic matter (OM) by microorganisms in thawing permafrost produces greenhouse gases. Terrestrial OM is transported into fjords through hydrological runoff, but it is unclear whether the microbial mechanisms of OM degradation on land persist after soils enter marine environments, which differ greatly in conditions and microbial communities. This question is particularly relevant for low-OM soils, which dominate Arctic landscapes and are more exposed to oxidants. Here, we compared OM-degrading capacity in permafrost-affected active layer soils and adjacent fjord sediments from Kongsfjorden, Svalbard, focusing on carbohydrate-active enzymes (CAZymes), which target some of the most abundant types of organic matter in soils. Using multi-omics approaches—metagenomics, metagenome-assembled genomes (MAGs), metabolomics, metatranscriptomics, and metaproteomics—we examined CAZyme presence, distribution, and activity. Despite environmental differences, both soils and sediments harbored diverse glycoside hydrolases and polysaccharide lyases, most of which showed evidence of activity. Verrucomicrobia expressed the highest number of CAZyme transcripts, indicating that they dominated active carbohydrate degradation in fjord sediments, while Acidobacteria and Actinobacteria were more active in soils. Notably, CAZymes in fjord sediments targeted primarily soil-derived OM, and the proportions of enzymes degrading terrestrial OM, marine OM, and microbial necromass—remnants of dead microbial cells were similar across both environments. These results suggest that microbial communities in both soils and fjord sediments are equipped to degrade carbohydrates, and that burial of terrestrial-derived OM in fjord sediments may not protect it from microbial breakdown under Arctic warming.

Chukwufumnanya, Abuah [University of Tennessee, Kn↗
DOE OSTI2022

Insight into co-hosts of nitrate reduction genes and antibiotic resistance genes in an urban river of the qinghai-tibet plateau

Microbial co-hosts of nitrate reduction genes (NRGs) and antibiotic resistance genes (ARGs) have been recently reported, but their ecology and biochemical role in urban waterways remain largely unknown. Here, we collected 69 surface water and sediment samples in the Huangshui River on the Qinghai-Tibet Plateau during the wet and dry season associated with comparatively low and high antibiotic levels. Using metagenomic sequencing, we retrieved 278 medium-to-high-quality metagenome-assembled genomes (MAGs) of NRG-ARG co-hosts, mainly belonging to the phyla Proteobacteria, Actinobacteriota, and Bacteroidota. Of microorganisms carrying ARGs, a high proportion (75.3?94.9%) also encoded NRGs, supporting nitrate reducing bacteria as dominant hosts of ARGs. Seasonal changes in antibiotic levels corresponded to significant variation in the relative abundance and community composition of NRG-ARG co-host in both water and sediments, resulting in a concomitant change in antibiotic resistance pathways. In contrast, the contribution of NRG-ARG co-hosts to nitrate reduction was stable between seasons. Further, we identify specific antibiotics (e.g., sulphonamides) and microbial taxa (e.g., Acinetobacter and Hafnia) that may disproportionately impact these relationships to serve as a basis for laboratory investigations into bioremediation strategies. Our study suggests that highly abundant nitrate reducing microorganisms in contaminated environments may also directly impact human health as carriers of antibiotic resistance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography

Abstract Wetlands store 20–30% of the world’s soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.

Environmental Sciences & Ecology↗