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At least 271 records · Page 15

Spatial Proteomics towards cellular Resolution

Introduction: Spatial biology is an emerging interdisciplinary field facilitating biological discoveries through the use of spatial omics technologies. Recent advancements in spatial transcriptomics, spatial genomics (e.g. genetic mutations and epigenetic marks), multiplexed immunofluorescence, and spatial metabolomics/lipidomics have enabled high-resolution spatial profiling of gene expression, genetic variation, protein expression, and metabolites/lipids profiles in tissue. These developments contribute to a deeper understanding of the spatial organization within tissue microenvironments at the molecular level. Areas covered: This report provides an overview of the untargeted, bottom-up mass spectrometry (MS)-based spatial proteomics workflow. It highlights recent progress in tissue dissection, sample processing, bioinformatics, and liquid chromatography (LC)-MS technologies that are advancing spatial proteomics toward cellular resolution. Expert opinion: The field of untargeted MS-based spatial proteomics is rapidly evolving and holds great promise. To fully realize the potential of spatial proteomics, it is critical to advance data analysis and develop automated and intelligent tissue dissection at the cellular or subcellular level, along with high-throughput LC-MS analyses of thousands of samples. In conclusion, achieving these goals will necessitate significant advancements in tissue dissection technologies, LC-MS instrumentation, and computational tools.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering a tumor-selective prodrug T-cell engager bispecific antibody for safer immunotherapy

T-cell engaging (TCE) bispecific antibodies are potent drugs that trigger the immune system to eliminate cancer cells, but administration can be accompanied by toxic side effects that limit dosing. TCEs function by binding to cell surface receptors on T cells, frequently CD3, with one arm of the bispecific antibody while the other arm binds to cell surface antigens on cancer cells. On-target, off-tumor toxicity can arise when the target antigen is also present on healthy cells. The toxicity of TCEs may be ameliorated through the use of pro-drug forms of the TCE, which are not fully functional until recruited to the tumor microenvironment. This can be accomplished by masking the anti-CD3 arm of the TCE with an autoinhibitory motif that is released by tumor-enriched proteases. Here, we solve the crystal structure of the antigen-binding fragment of a novel anti-CD3 antibody, E10, in complex with its epitope from CD3 and use this information to engineer a masked form of the antibody that can activate by the tumor-enriched protease matrix metalloproteinase 2 (MMP-2). We demonstrate with binding experiments and in vitro T-cell activation and killing assays that our designed prodrug TCE is capable of tumor-selective T-cell activity that is dependent upon MMP-2. Furthermore, we demonstrate that a similar masking strategy can be used to create a pro-drug form of the frequently used anti-CD3 antibody SP34. This study showcases an approach to developing immune-modulating therapeutics that prioritizes safety and has the potential to advance cancer immunotherapy treatment strategies.

60 APPLIED LIFE SCIENCES↗

The role of non-standard translation in Candida albicans pathogenesis

ABSTRACT Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.

Bezerra, Ana Rita (ORCID:0000000346131711)↗

Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize

Root-associated microbiomes in the rhizosphere (rhizobiomes) are increasingly known to play an important role in nutrient acquisition, stress tolerance, and disease resistance of plants. However, it remains largely unclear to what extent these rhizobiomes contribute to trait variation for different genotypes and if their inclusion in the genomic selection protocol can enhance prediction accuracy. To address these questions, we developed a microbiome-enabled genomic selection method that incorporated host SNPs and amplicon sequence variants from plant rhizobiomes in a maize diversity panel under high and low nitrogen (N) field conditions. Our cross-validation results showed that the microbiome-enabled genomic selection model significantly outperformed the conventional genomic selection model for nearly all time-series traits related to plant growth and N responses, with an average relative improvement of 3.7%. The improvement was more pronounced under low N conditions (8.4–40.2% of relative improvement), consistent with the view that some beneficial microbes can enhance N nutrient uptake, particularly in low N fields. However, our study could not definitively rule out the possibility that the observed improvement is partially due to the amplicon sequence variants being influenced by microenvironments. Using a high-dimensional mediation analysis method, our study has also identified microbial mediators that establish a link between plant genotype and phenotype. Some of the detected mediator microbes were previously reported to promote plant growth. The enhanced prediction accuracy of the microbiome-enabled genomic selection models, demonstrated in a single environment, serves as a proof-of-concept for the potential application of microbiome-enabled plant breeding for sustainable agriculture.

60 APPLIED LIFE SCIENCES↗

Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground

Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and 13 C enrichment in microorganisms, highlighting the potential to directly couple D 2 O or 13 C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.

36 MATERIALS SCIENCE↗

MECHANISMS OF RADIATION CARCINOGENESIS: WHAT IS REALLY INDUCED?

Abstract It has been difficult to understand why the relative risk for cancer decreases with an increase in time since an exposure to radiation. It was recently recognized that this decline can be explained by a parallel shift of the age-related cancer mortality curve toward younger ages. In fact, it has been known for many years that mouse survival curves exhibit a parallel shift toward younger ages following an exposure to radiation, but it was not recognized that the mutation induction theory is incompatible with this parallel shift. This is because a parallel shift in the survival curve implies that all the irradiated individuals are affected, but the mutation induction theory assumes that only a fraction of the irradiated individuals is affected following an exposure to radiation. Thus, it seems likely that the target of radiation action, which leads to carcinogenesis, is not restricted to epithelial cells but includes all of the surrounding cells leading to an altered microenvironment. Since it is repeatedly observed that radiation-exposed normal tissues can stimulate transplanted or spontaneously arising tumor cells to grow faster, worsen the malignant phenotypes and finally kill the host earlier than usual, an exposure to radiation seems most likely to cause tissue inflammation, which creates conditions favorable for the growth of spontaneously arising tumor cells. This new concept suggests that it might be possible to attenuate the extent of radiation carcinogenesis by intervening in tissue inflammatory processes.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Learning Grain-Boundary Segregation: From First Principles to Polycrystals

The segregation of solute atoms at grain boundaries (GBs) can strongly impact the structural and functional properties of polycrystals. Yet, due to the limited availability of simulation tools to study polycrystals at the atomistic scale (i.e., interatomic potentials), there is a minimal understanding of the variation of solute segregation tendencies across the very complex space of GB microenvironments and the large range of alloys in which it can occur. Here, we develop an algorithmic framework that can directly learn the full spectrum of segregation energies for a metal solute atom in a metal polycrystal from ab initio methods, bypassing the need for alloy interatomic potentials. This framework offers a pathway to a comprehensive catalog of GB solute segregation with quantum accuracy, for the entire alloy space. As an initial demonstration in this pursuit, we build an extensive GB segregation database for aluminum-based alloys across the periodic table, including dozens of alloys for which there are substantially no prior data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Constitutive down‐regulation of liguleless alleles in sorghum drives increased productivity and water use efficiency

Plant architecture influences the microenvironment throughout the canopy layer. Plants with a more erect leaf architecture allow for an increase in planting densities and allow more light to reach lower canopy leaves. This is predicted to increase crop carbon assimilation. Frictional resistance to wind reduces air movement in the lower canopy, resulting in higher humidity. By increasing the proportion of canopy photosynthesis in the more humid lower canopy, gains in the efficiency of water use might be expected, although this may be slightly offset by the more open erectophile form canopy. An anatomical feature in members of the Poaceae family that impacts leaf angle is the articulated junction of the sheath and blade, which also bares the ligule and auricles. Mutants, which lack ligules and auricles, show no articulation at this junction, resulting in leaves that are near vertical. In maize, these phenotypes termed liguleless result from null mutations of genes: ZmLG1 (Zm00001eb67740) and ZmLG2 (Zm00001eb147220). In sorghum, SbiRTx430.06G264300 (SbLG1) and SbiRTx430.03G392300 (SbLG2) are annotated as the respective maize homologues. A hair-pin element designed to down-regulate both SbLG1 and SbLG2 was introduced into the grain sorghum genotype RTx430. Derived transgenic events harbouring the hair-pin failed to develop ligules and displayed reduced leaf angles to the vertical, but less vertical than in null mutations. Under field settings, plots sown with these sorghum events having an erect architecture phenotype displayed an increase in photosynthesis in lower canopy levels, which led to increases in above-ground biomass and seed yield, without an increase in water use.

59 BASIC BIOLOGICAL SCIENCES↗

Stiffness anisotropy coordinates supracellular contractility driving long-range myotube-ECM alignment

The ability of cells to organize into tissues with proper structure and function requires the effective coordination of proliferation, migration, polarization, and differentiation across length scales. Skeletal muscle is innately anisotropic; however, few biomaterials can emulate mechanical anisotropy to determine its influence on tissue patterning without introducing confounding topography. Here, we demonstrate that substrate stiffness anisotropy coordinates contractility-driven collective cellular dynamics resulting in C2C12 myotube alignment over millimeter-scale distances. When cultured on mechanically anisotropic liquid crystalline polymer networks (LCNs) lacking topography, C2C12 myoblasts collectively polarize in the stiffest direction. Cellular coordination is amplified through reciprocal cell-ECM dynamics that emerge during fusion, driving global myotube-ECM ordering. Conversely, myotube alignment was restricted to small local domains with no directional preference on mechanically isotropic LCNs of the same chemical formulation. These findings provide valuable insights for designing biomaterials that mimic anisotropic microenvironments and underscore the importance of stiffness anisotropy in orchestrating tissue morphogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

High-precision chemical quantum sensing in flowing monodisperse microdroplets

A method is presented for high-precision chemical detection that integrates quantum sensing with droplet microfluidics. Using nanodiamonds (ND) with fluorescent nitrogen-vacancy (NV) centers as quantum sensors, rapidly flowing microdroplets containing analyte molecules are analyzed. A noise-suppressed mode of optically detected magnetic resonance is enabled by pairing controllable flow with microwave control of NV electronic spins, to detect analyte-induced signals of a few hundredths of a percent of the ND fluorescence. Using this method, paramagnetic ions in droplets are detected with low limit-of-detection using small analyte volumes, with exceptional measurement stability over >10 3 s. In addition, these droplets are used as microconfinement chambers by co-encapsulating ND quantum sensors with various analytes such as single cells, suggesting wide-ranging applications including single-cell metabolomics and real-time intracellular measurements from bioreactors. Important advances are enabled by this work, including portable chemical testing devices, amplification-free chemical assays, and chemical imaging tools for probing reactions within microenvironments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

The soil microbiome is an invaluable component of the biosphere and critical for ecosystem functions, including biogeochemical cycling, soil-atmosphere gas exchange, degradation of toxic compounds, and promotion of plant growth and stress resistance/resilience. An improved understanding of the soil microbiome will help with predicting how these processes respond to external perturbations, and with harnessing beneficial aspects of the soil microbiome for agronomic applications such as crop amendments. However, the extensive taxonomic and functional diversity inherent within the soil microbiome hinders efficient analysis of this system. Microbial biodiversity in soils is orders of magnitude greater than other commonly studied systems such as the human gut microbiome (Blum, Zechmeister-Boltenstern, and Keiblinger 2019; Berendsen, Pieterse, and Bakker 2012). Thousands of microbial taxa may be found in a single gram of soil (Roesch et al. 2007), and high rates of gene flow and mutation further promote microbial diversification (Sergaki et al. 2018). Concomitantly, functional diversity in soil is similarly extensive. Soil is a heterogeneous mixture of microenvironments with defined physical and chemical attributes (Bach et al. 2018), within which numerous microbial guilds of distinct life-strategies and metabolic capacities can be found (Perez-Garcia, Lear, and Singhal 2016; H.-S. Song et al. 2014). Furthermore, the soil microbiome harbors a significant fraction of rare and/or quiescent members (Blagodatskaya and Kuzyakov 2013) that exist below the threshold of detection of current technologies. Such rare taxa may make significant contributions to process rates (Shade and Gilbert 2015; Dawson et al. 2017), but their scarcity complicates their identification and analysis. Finally, the vast amounts of information generated through holistic analyses of soil communities represent an intense computational burden (Scholz, Lo, and Chain 2012; Prosser 2015) that precludes assessment of the complete functional and taxonomic diversity contained in this ecosystem.

Naylor, Dan T.↗

Mass spectrometry imaging of natural carbonyl products directly from agar-based microbial interactions using 4-APEBA derivatization

Aliphatic carboxylic acids, aldehydes, and ketones play diverse roles in microbial adaptation to their microenvironment, from excretion as toxins to adaptive metabolites for membrane fluidity. However, the spatial distribution of these molecules throughout biofilms and how microbes in these environments exchange these molecules remain elusive for many of these bioactive species due to inefficient molecular imaging strategies. Herein, we apply on-tissue chemical derivatization (OTCD) using 4-(2-((4-bromophenethyl)dimethylammonio)ethoxy)benzenaminium dibromide (4-APEBA) on a co-culture of a soil bacterium (Bacillus subtilis NCIB 3610) and fungus (Fusarium sp. DS 682) grown on agar as our model system. Using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), we spatially resolved more than 300 different metabolites containing carbonyl groups within this model system. Various spatial patterns are observable in these species, which indicate possible extracellular or intercellular processes of the metabolites and their up- or downregulation during microbial interaction. The unique chemistry of our approach allowed us to bring additional confidence in accurate carbonyl identification, especially when multiple isomeric candidates were possible, and this provided the ability to generate hypotheses about the potential role of some aliphatic carbonyls in this B. subtilis/Fusarium sp. interaction. The results shown here demonstrate the utility of 4-ABEBA-based OTCD MALDI-MSI in probing interkingdom interactions directly from microbial co-cultures, and these methods will enable future microbial interaction studies with expanded metabolic coverage.

4-APEBA↗

Is the Chemisorbed CO 2 in Ionic Liquid Electrolytes Active for Electrochemical Utilization? A Case Study on Carboxylate and Carbamate Speciation

This study examines the activity of chemisorbed CO 2 species in the microenvironment formed by bifunctional ionic liquids (ILs) in the reactive capture and conversion (RCC) of CO 2 to CO on silver. Comparative electroanalytical measurements with imidazolium based ILs were performed to probe the impact of electrostatic interactions, anion and cation basicity, and hydrogen bonding on RCC. Particularly, ILs with 1-ethyl-3-methylimidazolium ([EMIM]+) and 1-ethyl-2,3-dimethylimidazolium ([EMMIM]+) cations and aprotic heterocyclic anions of 2-cyanopyrrolide ([2-CNpyr]) and 1,2,4-triazolide ([124-Triz]) were examined for RCC. It was found that anion–CO 2 carbamate complexes facilitate RCC at significantly lower overpotentials compared to cation–CO 2 carboxylate complexes. Additionally, [EMIM]+ was found to better stabilize anion–CO 2 complexes at the interface than [EMMIM]+. Furthermore, it was found that 2-CNpyrH that naturally forms during CO 2 absorption competes for electrode surface adsorption with the anion–CO 2 carbamate complex, thereby reducing the electrochemical activity of the anion–CO 2 complex. These results highlight the importance of IL structure in tuning the interfacial interactions and suggest that ILs with anion-dominated CO 2 chemisorption enhances CO 2 utilization in RCC applications.

Coskun, Oguz Kagan [Case Western Reserve Univ., Cl↗

Targeting CCL2/CCR2 Signaling Overcomes MEK Inhibitor Resistance in Acute Myeloid Leukemia

Emerging evidence underscores the critical role of extrinsic factors within the microenvironment in protecting leukemia cells from therapeutic interventions, driving disease progression, and promoting drug resistance in acute myeloid leukemia (AML). This finding emphasizes the need for the identification of targeted therapies that inhibit intrinsic and extrinsic signaling to overcome drug resistance in AML. We performed a comprehensive analysis utilizing a cohort of ~300 AML patient samples. This analysis encompassed the evaluation of secreted cytokines/growth factors, gene expression, and ex vivo drug sensitivity to small molecules. Our investigation pinpointed a notable association between elevated levels of CCL2 and diminished sensitivity to the MEK inhibitors (MEKi). We validated this association through loss-of-function and pharmacologic inhibition studies. Further, we deployed global phosphoproteomics and CRISPR/Cas9 screening to identify the mechanism of CCR2-mediated MEKi resistance in AML. Our multifaceted analysis unveiled that CCL2 activates multiple prosurvival pathways, including MAPK and cell-cycle regulation in MEKi-resistant cells. Employing combination strategies to simultaneously target these pathways heightened growth inhibition in AML cells. Both genetic and pharmacologic inhibition of CCR2 sensitized AML cells to trametinib, suppressing proliferation while enhancing apoptosis. These findings underscore a new role for CCL2 in MEKi resistance, offering combination therapies as an avenue to circumvent this resistance. Our study demonstrates a compelling rationale for translating CCL2/CCR2 axis inhibitors in combination with MEK pathway-targeting therapies, as a potent strategy for combating drug resistance in AML. This approach has the potential to enhance the efficacy of treatments to improve AML patient outcomes.

60 APPLIED LIFE SCIENCES↗

A vision of immuno-oncology: the Siena think tank of the Italian Network for Tumor Biotherapy (NIBIT) foundation

The yearly Think Tank Meeting of the Italian Network for Tumor Biotherapy (NIBIT) Foundation, brings together in Siena, Tuscany (Italy), experts in immuno-oncology to review the learnings from current immunotherapy treatments, and to propose new pre-clinical and clinical investigations in selected research areas. While immunotherapies in non-small cell lung cancer and melanoma led to practice changing therapies, the same therapies had only modest benefit for patients with other malignancies, such as mesothelioma and glioblastoma. One way to improve on current immunotherapies is to alter the sequence of each combination agent. Matching the immunotherapy to the host’s immune response may thus improve the activity of the current treatments. A second approach is to combine current immunotherapies with novel agents targeting complementary mechanisms. Identifying the appropriate novel agents may require different approaches than the traditional laboratory-based discovery work. For example, artificial intelligence-based research may help focusing the search for innovative and most promising combination partners. Novel immunotherapies are needed in cancer patients with resistance to or relapse after current immunotherapeutic drugs. Such new treatments may include targeted agents or monoclonal antibodies to overcome the immune-suppressive tumor microenvironment. The mode of combining the novel treatments, including vaccines, needs to be matched to the patient’s immune status for achieving the maximum benefit. In this scenario, specific attention should be also paid nowadays to the immune intersection between COVID-19 and cancer.

60 APPLIED LIFE SCIENCES↗

Data for "Constitutive Down-Regulation of Liguleless Alleles in Sorghum Drives Increased Productivity and Water Use Efficiency"

Plant architecture influences the microenvironment throughout the canopy layer. Plants with a more erect leaf architecture allow for an increase in planting densities and allow more light to reach lower canopy leaves. This is predicted to increase crop carbon assimilation. Frictional resistance to wind reduces air movement in the lower canopy, resulting in higher humidity. By increasing the proportion of canopy photosynthesis in the more humid lower canopy, gains in the efficiency of water use might be expected, although this may be slightly offset by the more open erectophile form canopy. An anatomical feature in members of the Poaceae family that impacts leaf angle is the articulated junction of the sheath and blade, which also bares the ligule and auricles. Mutants, which lack ligules and auricles, show no articulation at this junction, resulting in leaves that are near vertical. In maize, these phenotypes termed liguleless result from null mutations of genes: ZmLG1 (Zm00001eb67740) and ZmLG2 (Zm00001eb147220). In sorghum, SbiRTx430.06G264300 (SbLG1) and SbiRTx430.03G392300 (SbLG2) are annotated as the respective maize homologues. A hair-pin element designed to down-regulate both SbLG1 and SbLG2 was introduced into the grain sorghum genotype RTx430. Derived transgenic events harbouring the hair-pin failed to develop ligules and displayed reduced leaf angles to the vertical, but less vertical than in null mutations. Under field settings, plots sown with these sorghum events having an erect architecture phenotype displayed an increase in photosynthesis in lower canopy levels, which led to increases in above-ground biomass and seed yield, without an increase in water use.

Genome Engineering↗

Investigating key cell types and molecules dynamics in PyMT mice model of breast cancer through a mathematical model

The most common kind of cancer among women is breast cancer. Understanding the tumor microenvironment and the interactions between individual cells and cytokines assists us in arriving at more effective treatments. Here, we develop a data-driven mathematical model to investigate the dynamics of key cell types and cytokines involved in breast cancer development. We use time-course gene expression profiles of a mouse model to estimate the relative abundance of cells and cytokines. We then employ a least-squares optimization method to evaluate the model’s parameters based on the mice data. The resulting dynamics of the cells and cytokines obtained from the optimal set of parameters exhibit a decent agreement between the data and predictions. We perform a sensitivity analysis to identify the crucial parameters of the model and then perform a local bifurcation on them. The results reveal a strong connection between adipocytes, IL6, and the cancer population, suggesting them as potential targets for therapies.

59 BASIC BIOLOGICAL SCIENCES↗

Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site

The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O 2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.

59 BASIC BIOLOGICAL SCIENCES↗