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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 685 records · Page 38
All sourcesNASA NTRSDOE OSTI
NASA NTRS2014

Updated Performance Evaluation of the ISS Water Processor Multifiltration Beds

The ISS Water Processor Assembly (WPA) produces potable water from a waste stream containing humidity condensate and urine distillate. The primary treatment process is achieved in the Multifiltration Beds, which include adsorbent media and ion exchange resin for the removal of dissolved organic and inorganic contaminants. Two Multifiltration Beds (MF Beds) were replaced on ISS in July 2010 after initial indication of inorganic breakthrough of the first bed and an increasing Total Organic Carbon (TOC) trend in the product water. The first bed was sampled and analyzed Sept 2011 through March 2012. The second MF Bed was sampled and analyzed June 2012 through August 2012. The water resident in the both beds was analyzed for various parameters to evaluate adsorbent loading, performance of the ion exchange resin, microbial activity, and generation of leachates from the ion exchange resin. Portions of the adsorbent media and ion exchange resin were sampled and subsequently desorbed to identify the primary contaminants removed at various points in the bed in addition to microbial analysis. Analysis of the second bed will be compared to results from the first bed to provide a comprehensive overview of how the Multifiltration Beds function on orbit. New data from the second bed supplements the analysis of the first bed (previously reported) and gives a more complete picture of breakthrough compounds, resin breakdown products, microbial activity, and difficult to remove compounds. The results of these investigations and implications to the operation of the WPA on ISS are documented in this paper.

Bowman, Elizabeth M.↗
DOE OSTI2022

Defensive symbiosis against giant viruses in amoebae

Protists are important regulators of microbial communities and key components in food webs with impact on nutrient cycling and ecosystem functioning. In turn, their activity is shaped by diverse intracellular parasites, including bacterial symbionts and viruses. Yet, bacteria–virus interactions within protists are poorly understood. Here, we studied the role of bacterial symbionts of free-living amoebae in the establishment of infections with nucleocytoplasmic large DNA viruses (Nucleocytoviricota). To investigate these interactions in a system that would also be relevant in nature, we first isolated and characterized a giant virus (Viennavirus, family Marseilleviridae) and a sympatric potential Acanthamoeba host infected with bacterial symbionts. Subsequently, coinfection experiments were carried out, using the fresh environmental isolates as well as additional amoeba laboratory strains. Employing fluorescence in situ hybridization and qPCR, we show that the bacterial symbiont, identified as Parachlamydia acanthamoebae, represses the replication of the sympatric Viennavirus in both recent environmental isolates as well as Acanthamoeba laboratory strains. In the presence of the symbiont, virions are still taken up, but viral factory maturation is inhibited, leading to survival of the amoeba host. The symbiont also suppressed the replication of the more complex Acanthamoeba polyphaga mimivirus and Tupanvirus deep ocean (Mimiviridae). Our work provides an example of an intracellular bacterial symbiont protecting a protist host against virus infections. The impact of virus–symbiont interactions on microbial population dynamics and eventually ecosystem processes requires further attention.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Interrogating the role of the milk microbiome in mastitis in the multi-omics era

There is growing interest in a functional understanding of milk-associated microbiota as there is ample evidence that host-associated microbial communities play an active role in host health and phenotype. Mastitis, characterized by painful inflammation of the mammary gland, is prevalent among lactating humans and agricultural animals and is associated with significant clinical and economic consequences. The etiology of mastitis is complex and polymicrobial and correlative studies have indicated alterations in milk microbial community composition. Recent evidence is beginning to suggest that a causal relationship may exist between the milk microbiota and host phenotype in mastitis. Multi-omic approaches can be leveraged to gain a mechanistic, molecular level understanding of how the milk microbiome might modulate host physiology, thereby informing strategies to prevent and ameliorate mastitis. In this paper, we review existing studies that have utilized omics approaches to investigate the role of the milk microbiome in mastitis. We also summarize the strengths and challenges associated with the different omics techniques including metagenomics, metatranscriptomics, metaproteomics, metabolomics and lipidomics and provide perspective on the integration of multiple omics technologies for a better functional understanding of the milk microbiome.

metabolomics↗
DOE OSTI2018

Factors controlling seasonal groundwater and solute flux from snow‐dominated basins

Abstract Critical zone influences on hydrologic partitioning, subsurface flow paths and reactions along these flow paths dictate the timing and magnitude of groundwater and solute flux to streams. To isolate first‐order controls on seasonal streamflow generation within highly heterogeneous, snow‐dominated basins of the Colorado River, we employ a multivariate statistical approach of end‐member mixing analysis using a suite of daily chemical and isotopic observations. Mixing models are developed across 11 nested basins (0.4 to 85 km 2 ) spanning a gradient of climatological, physical, and geological characteristics. Hydrograph separation using rain, snow, and groundwater as end‐members indicates that seasonal contributions of groundwater to streams is significant. Mean annual groundwater flux ranges from 12% to 33% whereas maximum groundwater contributions of 17% to 50% occur during baseflow. The direct relationship between snow water equivalent and groundwater flux to streams is scale dependent with a trend toward self‐similarity when basins exceed 5.5 km 2 . We find groundwater recharge increases in basins of high relief and within the upper subalpine where maximum snow accumulation is coincident with reduced conifer cover and lower canopy densities. The mixing model developed for the furthest downstream site did not transfer to upstream basins. The resulting error in predicted stream concentrations points toward weathering reactions as a function of source rock and seasonal shifts in flow path. Additionally, the potential for microbial sulfate reduction in floodplain sediments along a low‐gradient, meandering portion of the river is sufficient to modify hillslope contributions and alter mixing ratios in the analysis. Soil flushing in response to snowmelt is not included as an end‐member but is identified as an important mechanism for release of solutes from these mountainous watersheds. End‐member mixing analysis used in combination with high‐frequency observations reveals important aspects of catchment hydrodynamics across scale.

Carroll, Rosemary W. H.↗
DOE OSTI2020

Metagenomic Alterations in Gut Microbiota Precede and Predict Onset of Colitis in the IL10 Gene-Deficient Murine Model

SUMMARY. Currently, predictive markers for the development andcourse of inflammatory bowel diseases (IBD) are not available. This study supports the notion that gut microbiome metagenomic profiles could be developed into a useful tool to assess risk and manage human IBD. BACKGROUND & AIMS: Inflammatory bowel diseases (IBD) are chronic inflammatory disorders where predictive bio-markers for the disease development and clinical course are sorely needed for development of prevention and early intervention strategies that can be implemented to improve clinical outcomes. Since gut microbiome alterations can reflect and/or contribute to impending host health changes, we examined whether gut microbiota metagenomic profiles would provide more robust measures for predicting disease outcomes in colitis-prone hosts. METHODS: Using the interleukin (IL) 10 gene-deficient (IL10KO) murine model where early life dysbiosis from antibiotic (cefoperozone [CPZ]) treated dams vertically transferred to pups increases risk for colitis later in life, we investigated temporal metagenomic profiles in the gut microbiota of post-weaning offspring and determined their relationship to even-tual clinical outcomes. RESULTS: Compared to controls, offspring acquiring maternalCPZ-induced dysbiosis exhibited a restructuring of intestinal microbial membership in both bacteriome and mycobiome that was associated with alterations in specific functional subsystems. Furthermore, among IL10 KO offspring fromCPZ-treated dams, several functional subsystems, particularly nitrogen metabolism, diverged between mice that developed spontaneous colitis (CPZ-colitis) versus those that did not (CPZ-no-colitis) at a time point prior to eventual clinical outcome. CONCLUSIONS: Our findings provide support that functional metagenomic profiling of gut microbes has potential and promise meriting further study for development of tools to assess risk and manage human IBD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Genome‐enabled exploration of microbial ecology and evolution in the sea: a rising tide lifts all boats

Summary As a young bacteriologist just launching my career during the early days of the ‘microbial revolution’ in the 1980s, I was fortunate to participate in some early discoveries, and collaborate in the development of cross‐disciplinary methods now commonly referred to as "metagenomics". My early scientific career focused on applying phylogenetic and genomic approaches to characterize ‘wild’ bacteria, archaea and viruses in their natural habitats, with an emphasis on marine systems. These central interests have not changed very much for me over the past three decades, but knowledge, methodological advances and new theoretical perspectives about the microbial world certainly have. In this invited ‘How we did it’ perspective, I trace some of the trajectories of my lab's collective efforts over the years, including phylogenetic surveys of microbial assemblages in marine plankton and sediments, development of microbial community gene‐ and genome‐enabled surveys, and application of genome‐guided, cultivation‐independent functional characterization of novel enzymes, pathways and their relationships to in situ biogeochemistry. Throughout this short review, I attempt to acknowledge, all the mentors, students, postdocs and collaborators who enabled this research. Inevitably, a brief autobiographical review like this cannot be fully comprehensive, so sincere apologies to any of my great colleagues who are not explicitly mentioned herein. I salute you all as well!

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2010

International Space Station USOS Potable Water Dispenser On-Orbit Functionality Versus Design

The International Space Station (ISS) currently provides potable water dispensing for rehydrating crewmember food and drinking packages. There is one system located in the United States On-orbit Segment (USOS) and one system in the Russian Segment. Shuttle mission STS-126 delivered the USOS Potable Water Dispenser (PWD) to ISS on ULF2; subsequent activation occurred on November 2008. The PWD is capable of supporting an ISS crew of six, but nominally supplies only half this crew size. The PWD design provides incremental quantities of hot and ambient temperature potable water to US food and beverage packages. PWD receives iodinated water from the US Water Recovery System (WRS) Fuel Cell Water Bus, which feeds from the Water Processing Assembly (WPA). The PWD removes the biocidal iodine to make the water potable prior to dispensing. A heater assembly contained within the unit supplies up to 2.0 L of hot water (65 to 93 ?C) every 30 min. During a single meal, this quantity of water supports three to four crewmembers? food rehydration and beverages. The unit design has a functional life expectancy of 10 years, with replacement of limited life items, such as filters. To date, the PWD on-orbit performance is acceptable. Since activation of the PWD, there were several differences between on-orbit functionality and expected performance of hardware design. The comparison of on-orbit functionality to performance of hardware design is discussed for the following key areas: 1) microbial contamination, 2) no-dispense and water leakage scenarios, and 3) under-dispense scenarios.

Toon, Katherine P.↗
NASA NTRSDate not supplied

A Lunar Ground Truth of Microbes that are Integral to Sustaining Biological Life Support Systems

A lunar outpost such as Gateway or a Mars transit vehicle will use a semi-closed to closed loop biological life support system (BLSS) adapted for microgravity and high levels of radiation. A moon habitat will likely exist under partial gravity conditions and sustained levels of high radiation as a semi-closed loop system able to get resources from Earth via Gateway. Additionally, the moon will act as a closed-loop testbed for Mars habitat operations and will employ various elements of in situ resource utilization (ISRU). Perhaps the longest running BLSS collective study to date is that of the European MELiSSA (Micro Ecological Life Support System Alternative) project, a circular life support system, established to gain knowledge on regenerative systems aimed at the highest degree of autonomy to produce food, water and oxygen from mission wastes. This setup has evaluated the use of discrete microbial compartments and a higher plant compartment to carry out the necessary life support functions to support crew. Such compartments utilize thermophilic anaerobes to break down human and inedible plant wastes, photoheterotrophic bacteria that can further metabolize volatile fatty acids, nitrifying bacteria that can convert ammonium to plant and microalgae available nitrates, and photoautotrophic bacteria and higher plants which will convert carbon dioxide to oxygen, purify water, and provide food for human consumption. This being the most advanced BLSS model example to date -aside from the Yuegong-1, Chinese Lunar Palace- with the most defined compartment composition, and the assumption that other BLSSs will build upon such models, it becomes relevant to study the effects of the lunar environment upon the microbes that are integral to a BLSS. In ramping up to advanced stage BLSS systems, relatively simple experiments can be conducted on Artemis missions using continuous culturing and sampling of the model microbes, subsequently subjected to DNA sequencing for mutational analysis monitoring and chemical analysis to assess the sustained ability to carry out their hallmark biochemical processes efficiently. A suite of microbes should be assessed, prioritizing those with the duel capacity to be utilized in an BLSS and the ability to biochemically facilitate ISRU goals, such as the ability to transform the biogeochemistry of Moon or Martian regolith into materials that can support crop growth or extract elements of industrial significance such as aluminum or iron.

Biological Life Support Systems↗
NASA NTRS2010

Microbial Anomalies Encountered on the International Space Station

Microorganisms in our living environments are unavoidable. A community of microbes arrived in space with the delivery of the first element of the International Space Station (ISS), attached to hardware and on the bodies of the humans tasked with the initial assembly missions. The risk that microorganisms could cause adverse effects in the health of both the human occupants of the ISS as well as the physical integrity of the station environment and life support systems has been both a driver and a function of engineering and operational controls. Scientists and engineers at NASA have gone to extensive measures to control microbial growth at levels safe for the crewmembers and the spacecraft environment. Many of these measures were initiated with the design of the spacecraft and its systems. Materials used in the ISS were tested for resistance to fungi, such as mold and a paint with a fungus-killing chemical was also used. Controlling the humidity of the air in the Station is also an effective way of discouraging microbe growth. The breathing air is reconditioned by the Environmental Control Life Support System (ECLSS) prior to distribution, utilizing High Efficiency Particulate Air (HEPA) filtration. Requirements restricting the accumulation of water condensate in the air handlers and habitable volume of the ISS were other safeguards added. Water for drinking and food rehydration is disinfected or filtered. A robust in-flight housekeeping regimen for the ISS significantly reduces inappropriate growth of microorganisms and includes a regular cleaning of accessible surfaces with disinfectant wipes. Most of these requirements were suggested by microbiologists to mitigate and possibly prevent many microbiological risks. In addition to these controls, before flight monitoring and analyses of the cabin air, exposed surfaces, water and food, consumables, and crew members are conducted to mitigate microbial risk to the crew and spacecraft. Many microbial risks are much easier to identify and resolve before launch than during space flight. Although the focus has been on prevention of microbiologically related, not all problems can be anticipated. A number of microbial anomalies have occurred on ISS. This paper will discuss the occurrences, root-cause investigations, and mitigation steps taken to remediate the contamination.

Bruce, Rebekah J.↗
DOE OSTI2021

Quantifying the influence of different biocrust community states and their responses to warming temperatures on soil biogeochemistry in field and mesocosm studies

Biocrusts influence soil biogeochemistry by fixing carbon (C) and nitrogen (N) and through leachate inputs to soils. Functional rates can vary among biocrust community states and in response to edaphic properties, heterotrophic microbial activity, and global change. Using soils and biocrusts from the Colorado Plateau, Utah, USA, we aimed to quantify the influence of early-successional (ES) and late-successional (LS) biocrust community states on soil biogeochemistry. In a field setting, we found soil was less “fertile” under ES than LS biocrust, but ES biocrust had a relative influence 1.3 times greater than LS biocrust on soil fertility. Leachate collected from LS biocrust had, on average, 6 times more organic C and 1.7 times more dissolved N than ES biocrust, but concentrations of phosphorus (P) and inorganic N did not differ among the two biocrust types. Here, to disentangle influences of biocrusts and soil properties on biogeochemical pools, we constructed mesocosms from homogenized soil and left the surface bare or covered with ES or LS biocrust, before assignment to ambient or warmed (+5 °C) temperature treatments for 3 months. Multivariate biogeochemical properties differed among cover types, yet all exhibited losses of P, N, and organic C and nearly half of the biogeochemical variables considered did not differ among cover types. Mesocosms with LS biocrust retained more dissolved N, supported 8 additional, significant correlations among biogeochemical pools of the biocrust and mineral soil layer on average, and lost fewer of these correlations under warming. Overall, while soils under LS biocrusts were more fertile (i.e., had higher nutrient concentrations) than under ES, we did not find evidence implicating leachate as the primary driver of this difference. Biocrust influences on soil fertility were greater when mineral soil nutrients were in lower concentrations, highlighting the value of even incipient biocrusts for dryland functioning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Composition and metabolism of microbial communities in soil pores

Delineation of microbial habitats within the soil matrix and characterization of their environments and metabolic processes are crucial to understand soil functioning, yet their experimental identification remains persistently limited. We combined single- and triple-energy X-ray computed microtomography with pore specific allocation of 13 C labeled glucose and subsequent stable isotope probing to demonstrate how long-term disparities in vegetation history modify spatial distribution patterns of soil pore and particulate organic matter drivers of microbial habitats, and to probe bacterial communities populating such habitats. Here we show striking differences between large (30-150 µm Ø) and small (4-10 µm Ø) soil pores in (i) microbial diversity, composition, and life-strategies, (ii) responses to added substrate, (iii) metabolic pathways, and (iv) the processing and fate of labile C. We propose a microbial habitat classification concept based on biogeochemical mechanisms and localization of soil processes and also suggests interventions to mitigate the environmental consequences of agricultural management.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Non-destructive quantification of anaerobic gut fungi and methanogens in co-culture reveals increased fungal growth rate and changes in metabolic flux relative to mono-culture

Abstract Background Quantification of individual species in microbial co-cultures and consortia is critical to understanding and designing communities with prescribed functions. However, it is difficult to physically separate species or measure species-specific attributes in most multi-species systems. Anaerobic gut fungi (AGF) (Neocallimastigomycetes) are native to the rumen of large herbivores, where they exist as minority members among a wealth of prokaryotes. AGF have significant biotechnological potential owing to their diverse repertoire of potent lignocellulose-degrading carbohydrate-active enzymes (CAZymes), which indirectly bolsters activity of other rumen microbes through metabolic exchange. While decades of literature suggest that polysaccharide degradation and AGF growth are accelerated in co-culture with prokaryotes, particularly methanogens, methods have not been available to measure concentrations of individual species in co-culture. New methods to disentangle the contributions of AGF and rumen prokaryotes are sorely needed to calculate AGF growth rates and metabolic fluxes to prove this hypothesis and understand its causality for predictable co-culture design. Results We present a simple, microplate-based method to measure AGF and methanogen concentrations in co-culture based on fluorescence and absorbance spectroscopies. Using samples of < 2% of the co-culture volume, we demonstrate significant increases in AGF growth rate and xylan and glucose degradation rates in co-culture with methanogens relative to mono-culture. Further, we calculate significant differences in AGF metabolic fluxes in co-culture relative to mono-culture, namely increased flux through the energy-generating hydrogenosome organelle. While calculated fluxes highlight uncertainties in AGF primary metabolism that preclude definitive explanations for this shift, our method will enable steady-state fluxomic experiments to probe AGF metabolism in greater detail. Conclusions The method we present to measure AGF and methanogen concentrations enables direct growth measurements and calculation of metabolic fluxes in co-culture. These metrics are critical to develop a quantitative understanding of interwoven rumen metabolism, as well as the impact of co-culture on polysaccharide degradation and metabolite production. The framework presented here can inspire new methods to probe systems beyond AGF and methanogens. Simple modifications to the method will likely extend its utility to co-cultures with more than two organisms or those grown on solid substrates to facilitate the design and deployment of microbial communities for bioproduction and beyond.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Sphingomonas clade and functional distribution with simulated climate change

Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R 2 = 0.465) and clade composition (R 2 = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Knowledge Graph of RB-Tnseq Data from Fitness Browser (KP-DP1)

Motivation: Predicting microbial gene fitness across environmental conditions remains a central challenge for predictive phenomics and autonomous experimentation. Fitness assays generate large volumes of genotype–phenotype measurements difficult to integrate with experimental metadata and biological function in a form that supports mechanistic reasoning. Knowledge graphs offer a semantic framework for unifying modalities and enabling context-aware inference. Results: We build GIMME (Graph Inference for Microbial Metabolism Exploration), a semantically grounded knowledge graph that unifies gene fitness measurements spanning 10 Pseudomonas species with experimental metadata and biological context. Media are decomposed into chemical components and experiments carry structured links to natural-language descriptions. The resulting graph supports two inference modes: (1) symbolic graph traversal to surface candidate gene–environment and gene–chemical associations, and (2) learned inference using heterogeneous graph neural networks that propagate information across neighborhoods. We formulate link regression over (gene, media, experiment) triplets, combining learned gene embeddings with pretrained LLM sourced text embeddings of node descriptions to predict gene fitness. We then augment a baseline MLP with an auxiliary message-passing encoder (GraphSAGE/GAT) that propagates information over gene–protein–function and media–chemical subgraphs, and fuse the two pathways with a gated residual connection. This approach produces strong agreement with held-out fitness measurements (GraphSAGE Pearson r 0.74) while also highlighting inference challenges in extreme-fitness regimes. We aggregate GAT edge-attention weights by relation type and layer to estimate which biological and environmental relations most influence fitness predictions. Conclusion: This work explores using knowledge graphs as “context graphs” for microbial phenotype prediction. They provide a rich substrate which enables explainable retrieval of supporting evidence, and provides a natural bridge to autonomous workflows that prioritize the next experiment.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Sedimentary Parameters Controlling Occurrence and Preservation of Microbial Mats in Siliciclastic Depositional Systems

Shallow-marine, siliciclastic depositional systems are governed by physical sedimentary processes. Mineral precipitation or penecontemporaneous cementation play minor roles. Today, coastal siliciclastic environments may be colonized by a variety of epibenthic, mat-forming cyanobacteria. Studies on microbial mats showed that they are not randomly distributed in modern tidal environments. Distribution and abundancy is mainly function of a particular sedimentary facies. Fine-grained sands composed of "clear" (translucent) quartz particles constitute preferred substrates for cyanobacteria. Mat-builders also favor sites characterized by moderate hydrodynamic flow regimes, which permit biomass enrichment and construction of mat fabrics without lethal burial of mat populations by fine sediments. A comparable facies relationship can be observed in ancient siliciclastic shelf successions from the terminal Neoproterozoic Nama Group, Namibia. Wrinkle structures that record microbial mats are present but sparsely distributed in mid- to inner shelf sandstones of the Nudaus Formation. The sporadic distribution of these structures reflects both the narrow ecological window that governs mat development and the distinctive taphonomic conditions needed to preserve the structures. These observations caution that statements about changing mat abundance across the Proterozoic-Cambrian boundary must be firmly rooted in paleoenvironmental and taphonomic analysis. Understanding the factors that influence the formation and preservation of microbial structures in siliciclastic regimes can facilitate exploration for biological signatures in Earth's oldest rocks. Moreover, insofar as these structures can be preserved on bedding surfaces and are not easily mimicked by physical processes, they constitute a set of biological markers that can be searched for on Mars by remotely controlled rovers.

Noffke, Nora↗
DOE OSTI2020

Viral elements and their potential influence on microbial processes along the permanently stratified Cariaco Basin redoxcline

Little is known about viruses in oxygen-deficient water columns (ODWCs). In surface ocean waters, viruses are known to act as gene vectors among susceptible hosts. Some of these genes may have metabolic functions and are thus termed auxiliary metabolic genes (AMGs). AMGs introduced to new hosts by viruses can enhance viral replication and/or potentially affect biogeochemical cycles by modulating key microbial pathways. Here we identify 748 viral populations that cluster into 94 genera along a vertical geochemical gradient in the Cariaco Basin, a permanently stratified and euxinic ocean basin. The viral communities in this ODWC appear to be relatively novel as 80 of these viral genera contained no reference viral sequences, likely due to the isolation and unique features of this system. We identify viral elements that encode AMGs implicated in distinctive processes, such as sulfur cycling, acetate fermentation, signal transduction, [Fe–S] formation, and N-glycosylation. These AMG-encoding viruses include two putative Mu-like viruses, and viral-like regions that may constitute degraded prophages that have been modified by transposable elements. Our results provide an insight into the ecological and biogeochemical impact of viruses oxygen-depleted and euxinic habitats.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A broad-host-range event detector: expanding and quantifying performance between Escherichia coli and Pseudomonas species

Modern microbial biodesign relies on the principle that well-characterized genetic parts can be reused and reconfigured for different functions. However, this paradigm has only been successful in a limited set of hosts, mostly comprised from common lab strains of Escherichia coli . It is clear that new applications such as chemical sensing and event logging in complex environments will benefit from new host chassis. This study quantitatively compared how the same chemical event logger performed across four strains and three different microbial species. An integrase-based sensor and memory device was operated by two representative soil Pseudomonads— Pseudomonas fluorescens SBW25 and Pseudomonas putida DSM 291. Quantitative comparisons were made between these two non-traditional hosts and two benchmark E. coli chassis including the probiotic Nissle 1917 and common cloning strain DH5α. The performance of sensor and memory components changed according to each host, such that a clear chassis effect was observed and quantified. These results were obtained via fluorescence from reporter proteins that were transcriptionally fused to the integrase and downstream recombinant region and via data-driven kinetic models. The Pseudomonads proved to be acceptable chassis for the operation of this event logger, which outperformed the common E. coli DH5α in many ways. This study advances an emerging frontier in synthetic biology that aims to build broad-host-range devices and understand the context by which different species can execute programmable genetic operations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Smart Microbial Cells Couple Catalysis and Sensing to Provide High-Throughput Selection of an Organophosphate Hydrolase

Enzyme engineering for gain of function requires navigating a large combinatorial sequence space efficiently. Typically, many mutations are needed to get significant improvements, while a single “bad” mutation can inactivate the enzyme. To establish high-throughput screening and achieve enhanced resolution between two variants, genetic libraries of the organophosphate hydrolase enzyme paraoxonase 1 (PON 1 ) were rapidly screened via an engineered positive-feedback circuit: a p-nitrophenol (PNP)-specific transcription factor (TF) regulated expression of PON 1 , which catalyzed paraoxon breakdown and PNP production. Rare active mutant colonies, picked by simple visual fluorescence of a PON 1 –green fluorescent protein (GFP) fusion, were characterized. Furthermore, in a single screening round, high (library-scale) throughput enabled the discovery of enhanced paraoxon degradation activity in PON 1 , including structurally unexpected mutations.

59 BASIC BIOLOGICAL SCIENCES↗