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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Aboveground woody biomass estimation of young bioenergy plantations of Populus and its hybrids using mobile (backpack) LiDAR remote sensing

Woody aboveground biomass (AGB) including short-rotation Populus is used as a feedstock for renewable and carbon-neutral bioenergy. While woody AGB can be estimated with allometric equations requiring labor-intensive field data, remote sensing technologies like mobile terrestrial light detection and ranging (LiDAR) can estimate woody AGB quickly and accurately. Therefore, the goals of this study were to develop a model to predict woody AGB of 2-year-old Populus spp. from three taxa (P. deltoides, P. deltoides × P. maximowiczii and P. deltoides × P. trichocarpa) using allometric (height and diameter at breast height (DBH)) or LiDAR-derived metrics from a mobile terrestrial (backpack) system. Likewise, we sought to compare LiDAR-estimated tree height and DBH with field-measured values. We found that a taxa-specific model containing LiDAR-measured tree height, crown volume, and taxa interactions with the height of the 10 th percentile, and the density of the lowest interval (density metric 0) explained 84 % of the variation in woody AGB with a root mean square error (RMSE) of 28.7 % and performed slightly better than the allometric model. The best model excluding taxa had a slightly higher RMSE but lower bias than the allometric model. LiDAR-derived tree heights were highly correlated with field-measured heights, but DBH could not be estimated accurately. Therefore, terrestrial mobile LiDAR systems can accurately estimate woody AGB and tree height of Populus in short rotation systems to aid in the fast and efficient quantification of woody bioenergy production and renewable energy resources.

AGB↗
DOE OSTI2025

Morphotype-resolved characterization of microalgal communities in a nutrient recovery process with ARTiMiS flow imaging microscopy

Microalgae-driven nutrient recovery represents a promising technology for phosphorus removal from wastewater while simultaneously generating biomass that can be valorized to offset treatment costs. As full-scale processes come online, system parameters including biomass composition must be carefully monitored to optimize performance and prevent culture crashes. In this study, flow imaging microscopy (FIM) was leveraged to characterize microalgal community composition in near real-time at a full-scale municipal wastewater treatment plant (WWTP) in Wisconsin, USA, and population and morphotype dynamics were examined to identify relationships between water chemistry, biomass composition, and system performance. Two FIM technologies, FlowCam and ARTiMiS, were evaluated as monitoring tools. ARTiMiS provided a more accurate estimate of total system biomass, and estimates derived from particle area as a proxy for biovolume yielded better approximations than particle counts. Deep learning classification models trained on annotated image libraries demonstrated equivalent performance between FlowCam and ARTiMiS, and convolutional neural network (CNN) classifiers proved significantly more accurate when compared to feature table-based dense neural network (DNN) models. Across a two-year study period, Scenedesmus spp. appeared most important for phosphorus removal, and were negatively impacted by elevated temperatures and increase in nitrite/nitrate concentrations. Chlorella and Monoraphidium also played an important role in phosphorus removal. For both Scenedesmus and Chlorella, smaller morphological types were more often associated with better system performance, whereas larger morphotypes likely associated with stress response(s) correlated with poor phosphorus recovery rates. Furthermore, these results demonstrate the potential of FIM as a critical technology for high-resolution characterization of industrial microalgal processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Using low-coverage whole genome sequencing (genome skimming) to delineate three introgressed species of buffalofish ( Ictiobus )

Consumption of buffalofish has been sporadically associated with Haff disease-like illnesses involving sudden onset muscle pain and weakness due to skeletal muscle rhabdomyolysis, but determination of precisely which species are associated with these illnesses has been impeded by a lack of species-specific DNA-based markers. Here, three closely related species of buffalofish native to the Mississippi River Basin (Ictiobus bubalus, Ictiobus cyprinellus and Ictiobus niger) that have previously proven genetically indistinguishable using both mitochondrial and nuclear single-locus sequencing were reliably discriminated using low-coverage whole genome sequencing (‘genome skimming’). Using 44 specimens representing the three species collected from the mid/upper (Missouri) and lower (Louisiana) regions of the species’ native ranges, the SISRS (Site Identification from Short Read Sequences) bioinformatics pipeline was adapted to (1) identify over 620Mbp of putatively homologous nuclear sequence data and (2) isolate over 140,000 single-nucleotide polymorphisms (SNPs) that supported accurate species delimitation, all without the use of a reference genome or annotation data. These sites were used to classify Ictiobus spp. samples with genome-skim data, along with a larger set (n = 67) where ultraconserved elements (UCEs) were sequenced. Analyses of whole mitochondrial data revealed more limited signal. Nearly all samples matched their purported species based on morphologic identification, but two Missouri samples morphologically identified as I. niger grouped with samples of I. bubalus, albeit with significant enrichment of I. niger SNPs. To our knowledge this is the first report of a DNA-based tool to reliably discriminate these three morphologically distinct species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.

Dirks, Alden C↗
DOE OSTI2025

Ultrafast Dynamics of Plasmon-Coupled Excitons in Semiconducting Nanoplatelets

Exciton-plasmon coupling in nanomaterials produces many relevant phenomena for photonics applications including increased light-matter interactions, enhanced radiative rates of quantum emitters, and coherent energy exchange. In the case of exciton coupling to surface plasmon polaritons (SPPs), dispersive interactions controlled by the wavevector of optical excitation create the opportunity for tunable optical emission. Strong temporal impacts on exciton lifetimes can also occur in coupled systems, creating the opportunity for ultrafast control of exciton lifetime via changes in electronic coupling magnitude to a dispersive SPP. The coupling strength can be impacted by the morphology of the nanomaterials. Here, in this study, we utilize colloidal semiconductor nanoplatelets deposited onto thin silver plasmonic films, and compare the results to semiconductor quantum dots deposited on the silver films. We map the dispersion of the coupled systems and measure the ultrafast transient absorption response of the coupled systems. Due to the larger interaction areas of the nanoplatelets that lie flat on the silver films, a greater degree of coupling is found for the nanoplatelets, and much faster temporal responses are found as compared to quantum dots. Fresnel theory calculations that incorporate heavy and light hole features can reproduce the dispersion of the nanoplatelet-silver film, and a simple three-state model is developed to provide insights into the nature of the coupling at different photon energies along the dispersion curve.

colloidal semiconductor nanoplatelets↗
DOE OSTI2022

Effect of Macro- and Microstructures on Catalytic Hydrogenolysis of Polyolefins

Here, polyethylenes of varying molecular weight and branch density, as well as polypropylenes of varying molecular weight and tacticity, were catalytically converted to lower-molecular-weight liquid products to showcase how these various properties in a mixed waste plastic stream could affect the final product. A Pt nanoparticle on a strontium titanate nanocuboid (Pt/STO) catalyst was used under solvent-free conditions in the presence of 170 psi of H 2 at 300 °C for hydrogenolysis. The initial molecular weight of polyethylene was found to have a moderate effect on the yield to the final product (ranging from 55 wt% for M n ~ 7600 Da to 67 wt% for M n ~ 50,950 Da). The microstructure, defined as the length and density of branches in a polymer, of higher-molecular-weight polymers was the dominant factor in determining the yield (ranging from 67 wt% for M n ~ 50,950 Da for linear low-density polyethylene (LLDPE) with C 2 branches to 97 wt% for M n ~ 38,850 Da for LLDPE with C 6 branches). The same products (M n = C 29 –C 46 , Ð = 1.1–1.6) and distribution of undesired light gases (C 1 –C 4 ≈ 90 mol%, C 5 –C 8 ≈ 10 mol%) are obtained from conversions of PE of varying molecular weight. The tacticity of polypropylene at a given molecular weight had a significant effect on the molecular weight of the final product, while not strongly affecting conversion. Hydrogenolysis of isotactic polypropylene (iPP) produced ≈C 18 with a wider polydispersity (Ð ~ 1.4) compared to the narrow ≈C 64 (Ð ~ 1.0) and ≈C 54 (Ð ~ 1.0) products from atactic (aPP) and syndiotactic (sPP) polypropylene, respectively. The stereochemistry of the methyl groups dictates the shape and structure of the polymer in the melt, which in turn affects how the hydrocarbon chain interacts with the catalyst surface, thereby impacting the number of C–C scissions. These results show how various characteristics such as the molecular weight and structure of a waste plastic stream could affect the final product.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Plasmons Enable Ultralow Threshold Solid-State Triplet Fusion Upconversion with a 2D Sensitizer

Solid-state triplet−triplet annihilation (TTA) upconversion has significant potential for application in light harvesting, optoelectronic devices, and bioimaging. However, the high optical powers required to achieve efficient upconversion have inhibited its adoption. In this work, we demonstrate plasmon-enhanced near-infrared (NIR)-to-blue TTA upconversion in a monolayer WSe2/organic heterojunction. Under far-field excitation, the device reaches a threshold of 19 mW/cm 2 and an external quantum efficiency (EQE) of 0.17% with an anti-Stokes shift of 1.1 eV. Plasmon excitation lowers the threshold to 0.9 mW/cm 2 and improves the EQE to 3.6%. We attribute the plasmon enhancement to surface plasmon polariton (SPP) near-field enhancement and dark-exciton absorption. Optimization of the WSe 2 transfer process is identified as a key factor for the device performance. This work demonstrates that plasmon excitation overcomes the low far-field absorption of 2D transition-metal dichalcogenide (TMD) sensitizers. Consequently, monolayer TMDs can achieve solid-state upconversion with a performance among the best reported.

2D materials↗
DOE OSTI2022

Dehydrogenation of Propane and n -Butane Catalyzed by Isolated PtZn 4 Sites Supported on Self-Pillared Zeolite Pentasil Nanosheets

Propene and 1,3-butadiene are important building-block chemicals that can be produced by dehydrogenation of propane and butane over Pt catalysts. The challenge is to develop highly active and selective catalysts that are resistant to deactivation by Pt sintering and coke formation. We have recently shown that these objectives can be met for propane dehydrogenation using atomically dispersed Pt atoms anchored to neighboring ≡SiOZn-OH groups bonded to the framework dealuminated zeolite BEA. In the present study, we demonstrate that significantly superior performance can be achieved by using self-pillared pentasil (SPP) zeolite nanosheets. Following catalyst reduction in H 2 , atomic-resolution, scanning transmission electron microscopy (STEM) and X-ray absorption spectroscopy (XAS) indicate that Pt is stabilized in structures well approximated as (≡Si-O-Zn) 4-5 Pt. These species are highly active, selective, and stable for propane dehydrogenation (PDH) to give propene and for n-butane dehydrogenation (BDH) to give 1,3-butadiene. No catalyst deactivation was observed after 12 days of time on stream, and the selectivity remained at nearly 100% for PDH conducted at 823 K and a weight hourly space velocity (WHSV) of 1,350 h -1 . The apparent rate coefficient for PDH over this catalyst is significantly higher than that reported previously for Pt-containing catalysts. For BDH at 823 K and a WHSV of 3560 h -1 , the selectivity to butene isomers and 1,3-butadiene is 98.9%, and the selectivity to 1,3-butadiene is 45%. Here, we propose that the high catalyst stability observed during PDH and BDH is a consequence of a large fraction of the Pt-containing centers being located on the external surface of the zeolite nanosheets, where nascent coke precursors can desorb before condensing to form coke.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Scrambling Signal Modularity in Bottom-up Assembled Synthetic Pseudomonas Consortia Reveals Robust Information Transfer

There is immense potential in crafting synthetic microbial communities for application in human health, agriculture, the environment, and even biomanufacturing where an appropriately constructed consortium can be assembled with tremendous biosynthetic or degradative capabilities. In many of these cases, bacterial signaling serves as a form of intercellular information transfer that guides the collective’s behavior. Such communication is complex, as many signals, signal disruptors, microbial species, physical barriers, and spatiotemporal constraints may be involved. Here, in this work, we demonstrate that a multisignal pathway for molecular information transfer within a consortium of several Pseudomonas spp. can be scrambled (genetically and organizationally) while the original message is still effectively conveyed. Assembled from the bottom up, we have employed two types of signaling molecules (i) a redox active secondary metabolite (rhizospheric signal, phloroglucinol), and (ii) a bacterial quorum sensing signal (3-oxo-C12 acylhomoserine lactone, AI-1). These signals can be intraconverted and acted upon by designated community members. We show how the order in which the signals are received, transduced, and subsequently transmitted can be rearranged with minimal impact on the intended outcome. In the consortial context, we found this messaging structure can be remarkably robust. Inspired by rhizospheric molecular signaling mechanisms, this work provides a conceptual framework for designing signaling and information transfer processes within assembled communities.

Biological and medical sciences↗
DOE OSTI2021

Contrasting Responses of Soil Inorganic Carbon to Afforestation in Acidic Versus Alkaline Soils

Afforestation is recommended as an effective approach for carbon sequestration and environmental benefits. However, it remains less clear, and sometimes controversial, regarding how afforestation may impact soil inorganic carbon (SIC), a crucial component of the ecosystem carbon pool. Here, using field data from 619 afforested plots and 163 control plots across northern China, we investigated the relative and absolute differences in SIC between afforested and corresponding control plots. Our results suggested that afforestation increased SIC in acidic soils, while decreased SIC in alkaline soils. Fitting a linear mixed model and further a structure equation model, we found that afforestation-induced soil pH change was the most significant factor regulating SIC responses. In particular, SIC was more sensitive to pH change in more arid areas, where both soil pH and SIC stocks were high. Other factors could indirectly affect SIC responses to afforestation through modulating soil pH and soil organic carbon (SOC) dynamics. Moreover, afforestation-induced SIC changes also varied considerably among different species of tree plantations and across different soil depths. Importantly, in plantations of Pinus sylvestris var. mongholica, Pinus tabuliformis, and Populus spp., changes in SIC caused by afforestation were even comparable to that in SOC. Overall, our findings provide a data-based understanding on the comprehensive soil carbon dynamics following afforestation and its underlying mechanisms. With the increased use of afforestation and reforestation as nature-based solutions to climate change, their associated impacts on SIC need to be taken into account, especially in SIC-rich areas.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms

Massive releases of organic substrates during marine algal blooms trigger growth of many clades of heterotrophic bacteria. Algal polysaccharides represent the most diverse and structurally complex class of these substrates, yet their role in shaping the microbial community composition is poorly understood. We investigated, whether polysaccharide utilization capabilities contribute to niche differentiation of Polaribacter spp. (class Flavobacteriia; known to include relevant polysaccharidedegraders) that were abundant during 2009–2012 spring algal blooms in the southern North Sea. We identified six distinct Polaribacter clades using phylogenetic and phylogenomic analyses, quantified their abundances via fluorescence in situ hybridization, compared metagenome-assembled genomes, and assessed in situ gene expression using metaproteomics. Four clades with distinct polysaccharide niches were dominating. Polaribacter 2-a comprised typical first responders featuring small genomes with limited polysaccharide utilization capacities. Polaribacter 3-a were abundant only in 2010 and possessed a distinct sulfated α-glucoronomannan degradation potential. Polaribacter 3-b responded late in blooms and had the capacity to utilize sulfated xylan. Polaribacter 1-a featured high numbers of glycan degradation genes and were particularly abundant following Chattonella algae blooms. These results support the hypothesis that sympatric Polaribacter clades occupy distinct glycan niches during North Sea spring algal blooms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cave Thiovulum ( Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O 2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O 2 and NO 3 - as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Development of a thermophilic coculture for corn fiber conversion to ethanol

Abstract The fiber in corn kernels, currently unutilized in the corn to ethanol process, represents an opportunity for introduction of cellulose conversion technology. We report here that Clostridium thermocellum can solubilize over 90% of the carbohydrate in autoclaved corn fiber, including its hemicellulose component glucuronoarabinoxylan (GAX). However, Thermoanaerobacterium thermosaccharolyticum or several other described hemicellulose-fermenting thermophilic bacteria can only partially utilize this GAX. We describe the isolation of a previously undescribed organism, Herbinix spp . strain LL1355, from a thermophilic microbiome that can consume 85% of the recalcitrant GAX. We sequence its genome, and based on structural analysis of the GAX, identify six enzymes that hydrolyze GAX linkages. Combinations of up to four enzymes are successfully expressed in T. thermosaccharolyticum . Supplementation with these enzymes allows T. thermosaccharolyticum to consume 78% of the GAX compared to 53% by the parent strain and increases ethanol yield from corn fiber by 24%.

09 BIOMASS FUELS↗
DOE OSTI2021

Monolignol acyltransferase for lignin p-hydroxybenzoylation in Populus

Plant lignification exhibits significant plasticity. Lignin in many species including Populus spp. has long been known decorated with p-hydroxybenzoates. However, the molecular basis for such structural modification remains undetermined. Here we report the identification and characterization of a Populus BAHD family acyltransferase that catalyzes monolignol p-hydroxybenzoylation, thus controlling the formation of p-hydroxybenzoylated lignin structures. We reveal that Populus acyltransferase PHBMT1 kinetically preferentially utilizes p-hydroxybenzoyl-CoA to acylate syringyl lignin monomer sinapyl alcohol in vitro. Consistently, disrupting PHBMT1 in Populus via CRISPR/Cas9 gene editing nearly completely depletes p-hydroxybenzoates of stem lignin; conversely, overexpression of PHBMT1 enhances stem lignin p-hydroxybenzoylation, suggesting PHBMT1 functions as a prime monolignol p-hydroxybenzoyltransferase in planta. Altering lignin p-hydroxybenzoylation significantly changes lignin solvent dissolution rate, indictive of its structural significance on lignin physiochemical properties. Identification of monolignol p-hydroxybenzoyltransferase offers a valuable tool for tailoring lignin structure and physiochemical properties and for engineering the industrially important platform chemical in woody biomass.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Large freshwater phages with the potential to augment aerobic methane oxidation

There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host–phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt

Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.

Sorensen, Patrick O↗
DOE OSTI2022

Borgs are giant genetic elements with potential to expand metabolic capacity

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions1, yet factors that modulate the activity of microorganisms performing this function remain poorly understood. Here we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins through studying groundwater, sediments and wetland soil where methane production and oxidation occur. Four curated, complete genomes are linear, up to approximately 1 Mb in length and share genome organization, including replichore structure, long inverted terminal repeats and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are highly divergent archaeal extrachromosomal elements with a distinct evolutionary origin. Gene sequence similarity, phylogeny and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as ‘Borgs’. We identified at least 19 different Borg types coexisting with Methanoperedens spp. in four distinct ecosystems. Borgs provide methane-oxidizing Methanoperedens archaea access to genes encoding proteins involved in redox reactions and energy conservation (for example, clusters of multihaem cytochromes and methyl coenzyme M reductase). These data suggest that Borgs might have previously unrecognized roles in the metabolism of this group of archaea, which are known to modulate greenhouse gas emissions, but further studies are now needed to establish their functional relevance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7±19.1 and 36.5±10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.

59 BASIC BIOLOGICAL SCIENCES↗