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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics

This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1–0.2 ppt and brackish 0.3–1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10–100 kyr old), MP (105–120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios

Seasonal floodplains in the Amazon basin are important sources of methane (CH 4 ), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH 4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH 4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH 4 fluxes. CH 4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH 4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH 4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH 4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH 4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH 4 oxidation pathways in mitigating CH 4 emissions in Amazonian floodplains.

16S rRNA sequencing↗
DOE OSTI2023

Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins

Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of TRs in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently, and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg–host associations and possibly cospeciation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling

Understanding CRISPR-Cas systems—the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks—is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical ‘rich-get-richer’ mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Physiological, genomic, and sulfur isotopic characterization of methanol metabolism by Desulfovibrio carbinolicus

Methanol is often considered as a non-competitive substrate for methanogenic archaea, but an increasing number of sulfate-reducing microorganisms (SRMs) have been reported to be capable of respiring with methanol as an electron donor. A better understanding of the fate of methanol in natural or artificial anaerobic systems thus requires knowledge of the methanol dissimilation by SRMs. In this study, we describe the growth kinetics and sulfur isotope effects of Desulfovibrio carbinolicus, a methanol-oxidizing sulfate-reducing deltaproteobacterium, together with its genome sequence and annotation. D. carbinolicus can grow with a series of alcohols from methanol to butanol. Compared to longer-chain alcohols, however, specific growth and respiration rates decrease by several fold with methanol as an electron donor. Larger sulfur isotope fractionation accompanies slowed growth kinetics, indicating low chemical potential at terminal reductive steps of respiration. In a medium containing both ethanol and methanol, D. carbinolicus does not consume methanol even after the cessation of growth on ethanol. Among the two known methanol dissimilatory systems, the genome of D. carbinolicus contains the genes coding for alcohol dehydrogenase but lacks enzymes analogous to methanol methyltransferase. We analyzed the genomes of 52 additional species of sulfate-reducing bacteria that have been tested for methanol oxidation. There is no apparent relationship between phylogeny and methanol metabolizing capacity, but most gram-negative methanol oxidizers grow poorly, and none carry homologs for methyltransferase (mtaB). Although the amount of available data is limited, it is notable that more than half of the known gram-positive methanol oxidizers have both enzymatic systems, showing enhanced growth relative to the SRMs containing only alcohol dehydrogenase genes. Thus, physiological, genomic, and sulfur isotopic results suggest that D. carbinolicus and close relatives have the ability to metabolize methanol but likely play a limited role in methanol degradation in most natural environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

16S and ITS Amplicon Sequencing Fastq files and metadata from PARCHED Panama Tropical Forest soils, 2019-2020,

Model projections predict tropical forests will experience longer periods of drought and more intense precipitation cycles under a changing climate. Such transitions have implications for structure-function relationships within microbial communities. We examine how chronic drying might reshape prokaryotic and fungal communities across four lowland forests in Panama with a wide variation in mean annual precipitation and soil fertility. Four sites were established across a 1000 mm span in mean annual precipitation (2335 to 3300 mm). We expected microbial communities at sites with lower MAP to be less sensitive to chronic drying than sites with higher MAP; while fungal communities to be more resistant to disturbance than prokaryotes. At each location, partial throughfall exclusion structures were established over 10 x 10 m plots to reduce direct precipitation input. Raw demultiplexed sequences (bacteria, archaea, fungal) from soil samples taken from PARCHED Panama Tropical Forest throughfall exclusion experiments. Files that contain 16S are sequences from prokaryotes, ITS indicates sequences from fungi. Compressed fastq files are contained in Field_PARCHED_ITS_fastq_2020.zip, Field_PARCHED_ITS_fastq_2019.zip, Field_PARCHED_16S_fastq_2020.zip, Field_PARCHED_16S_fastq_2019.zip.There are four sites across the isthmus of Panama, each with 4 control and 4 exclusion plots. Throughfall exclusion shelters were built to intercept 50% of throughfall precipitation that hits the soil. Samples were taken on May 2019 and Jan 2020 from 0-10 cm and 10-20 cm depth approximately 9 and 18 months after shelter installation. Metadata and sample IDs for fastq files for 2019 sampling are within Field_PARCHED_Metadata_2019_ITS.csv and Field_PARCHED_Metadata_2019_16S.csv. The metadata for both 16S and ITS fastq files for January 2020 is included in Field_PARCHED_Metadata_2020.csv. No data processing or QA/QC was done on the raw data. Data processing example provided in R notebook file.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Editorial: Viruses, Genetic Exchange, and the Tree of Life

We live in exciting times for microbiology research. The significant technological and scientific advancements in the past decades have now enabled scientists to pursue discovery and description of novel microbial and viral linages from previously uncharted Earth habitats. Two such discoveries are particularly exciting and noteworthy in this regard. First, the discovery of the first ‘giant virus’, Acanthamoeba polyphaga mimivirus, in 2003, and several others thereafter, posed intriguing questions regarding virus origins, evolution, classification, and their place in the ‘tree of life’. Second, the discoveries of ‘Lokiarchaeota’ and several other closelyrelated archaeal members that encode several eukaryote-specific proteins challenged the threedomain canonical structure of the tree of life. These discoveries have reopened debates on central questions in evolutionary biology research such as the origin of viruses, the origin of eukaryotes, evolutionary relationship between Archaea and Eukarya, and the structure and topology of the tree of life. In this Research Topic, we received a broad range of contributions addressing these and other related questions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Novel Microbial Based Enzymatic CO 2 Fixation Mechanisms

The broad, long term goal of the research is to provide insight into the mechanism of novel carboxylation reactions catalyzed by enzymes involved in bacterial alkene, ketone, and epoxide metabolism. Novel convergent pathways in the model microorganism Xanthobacter autotrophicus have been described in which epoxides produced by alkene oxidation and ketones produced by the oxidation of alcohols are further carboxylated and utilized in energy yielding pathways. Both alkene/epoxide and alcohol/ketone pathways involve distinct carboxylases with unique molecular properties and cofactor requirements that represent alternative mechanisms of CO 2 fixation. The main focus and aims of this project is to provide structural basis for the mechanistic understanding of the reactions catalyzed by 2-ketopropyl coenzyme M oxidoreductase / carboxylase and acetone carboxylase, the terminal steps in the convergent pathways of alkene/epoxide and alcohol ketone metabolism in X. autotrophicus strain Py2. Interestingly, coenzyme M (CoM), the simplest known organic coenzyme, has been shown to have a central role in the pathway of alkene/epoxide carboxylation. Prior to this discovery CoM was thought only to be involved in methanogenesis in archaea. In addition to the carboxylation mechanisms, we are examining the enzymology of the biosynthesis of CoM in bacteria and we have already determined that it is biochemically distinct from that of CoM synthesized by methanogens. The proposed studies will reveal new and unique insights into CO 2 fixation pathways and carboxylation chemistry. We are utilizing a multidisciplinary approach involving kinetic studies, site-specific amino acid substitution studies, and the determination of high-resolution structures of enzymes in the presence of substrate analogs and mechanism base inhibitors to ascertain information concerning the biochemical mechanisms of enzyme catalyzed reactions. Within the context of the mission of the Department of Energy and the core activities of the Energy Biosciences, the results obtained in the study will reveal new insights into these novel carboxylation reactions and will provide the basis for the comparison of the mechanism of these interesting enzymes to other well-characterized biological mechanisms for CO 2 fixation and carboxylation. Knowledge concerning the mechanism of these enzymes provides the basis for an increased fundamental understanding of carboxylation chemistry that could contribute to future mechanisms for CO 2 capture and fixation and, in turn, to mitigating the effects of increasing concentrations of CO 2 on global climate change.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Plant Single-Cell Solutions for Energy and the Environment (Second Workshop Report)

Plants are important sources of energy and materials, and they collectively represent a critical component of Earth’s ecosystem. With increasing environmental stresses due to climate change and intensive agricultural practices, the need for resilient plants is greater than ever before. To secure plant resources for bioenergy, biomaterials, food, and ecosystem adaptation, a deeper understanding of the fundamental biology of plants at a cellular level is urgently needed. Plants contain a multitude of specialized cell types that compose tissues and organs. Pathogens often target specific cell types within plants, and the response of one cell to a particular stimulus is likely to be distinct from its neighbor because of underlying molecular and contextual differences. Understanding how these responses are distributed among cells, the main goal of single-cell approaches, will substantially enhance our ability to use targeted engineering for improving plant productivity and resilience. Furthermore, single-cell approaches are necessary to understand the interactions between plants and other ecosystem members such as fungi, bacteria, and archaea. Unlocking these gene-response mechanisms at a cellular level can improve our ability to adapt plants to environmental stresses, increasing their utility as feedstocks for biomaterials and bioenergy. Recent advances in high-throughput sequencing, mass spectrometry, microfluidics and miniaturization, artificial intelligence and machine learning, and bioinformatics have greatly improved our ability to detect and understand processes at a cellular level. In mammalian systems, single-cell transcriptomics has already led to many advances, such as newly identified cell types and cell-targeted treatment of diseases, and mass spectrometry-based single-cell proteomics has recently been demonstrated as a promising emerging technology. However, plant single-cell omics has lagged behind mammalian approaches due to the high cost of the technologies relative to available resources and to the innate biological features of plants, including the complexity of the cell wall and polyploidy. To better understand how single-cell methods could enable plant science, Lawrence Berkeley National Laboratory (Berkeley Lab) hosted a workshop on April 29, 2021, that brought together a diverse group of leaders in plant and/or single-cell biology. Attendees represented federal research programs and domestic and international academic institutions. During the workshop, three presenters described the current state of research in both experimental and computational approaches. While the focus of the workshop was on factors preventing plant biology researchers from fully adopting single-cell methodologies, workshop participants agreed that most barriers could be overcome with focused, strategic investment and coordinated efforts among institutions leading to significant scientific discoveries that would be difficult to obtain using more conventional technologies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multisystem feedbacks from a changing climate: Do altered hydrological dynamics control vadose zone carbon nutrient cycling and storage in shallow aquifer systems?

The vadose zone, which extends from upper soils to the subsurface water table, consists of many distinct habitats (including the critical zone), each with its own physical characteristics. Upper soils are typically richer in organic carbon chemical diversity and concentration, while deeper portions near the water table have less labile carbon and a greater percentage of humic acids and other long-lived organics. The availability of carbon and oxygen constrain the habitability of these zones. Typically, microorganisms (bacteria, archaea, and fungi) extend throughout the vadose zone and potentially deeper into the bedrock, while higher eukaryotes (i.e., arthropods and plants) are limited to the surficial soils. An exception to this is deep taproots of some tree species that can extend tens of meters into the subsurface. In subsurface systems, microbial metabolisms are constrained by the availability of carbon (organic and inorganic) and electron acceptors.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Understanding Soil Microbial Sources of Nitrous Acid and their Effect on Carbon-Nitrogen Cycle Interactions

Descriptions of soil emissions of reactive nitrogen (NO y ) in climate models are underdeveloped or non-existent, due to the fact that details of the mechanisms leading to nitrous acid (HONO) and nitrogen di-oxide (NO 2 ) formation in soil are lacking. This represents a major gap in our understanding of a significant land-atmosphere interaction that prevents us from scaling these processes from the laboratory scale to the ecosystem and global scales. There is a critical need to include these mechanisms into climate models since NO y controls the oxidative capacity of the atmosphere and the lifetime of greenhouse gases and the rate of secondary aerosol formation that directly and indirectly affect climate. The first objective of this proposal is to conduct laboratory and field measurements of NO y fluxes from diverse soil types and determine the mechanism of biogenic NO y formation. The working hypothesis based on preliminary data is that soil HONO and NO 2 is ultimately derived from ammonia-oxidizing archaea (AOA) and bacteria (AOB) that are widespread, but whose abundance varies across ecosystems. In the case of NO 2 , reactive oxygen species derived from iron-containing minerals and heterotrophic bacteria drive NO-to-NO 2 conversion. The approach is to link soil fluxes of HONO and NO 2 to AOA, AOB, and other heterotrophs using a combination of laboratory and field experiments, isotopic analysis, and molecular techniques to address how variability in land surfaces and edaphic properties impact emissions. In addition, we will determine the effect of HONO and NO 2 on nitrogen immobilization and the photo-oxidative capacity of soil. The working hypothesis is that HONO uptake in soil will be a source of nitrosonium and hydroxyl radical that will lead to thermal- and photodegradation of soil organic matter to CO 2 and CO, and the incorporation of N in soil organic matter. We will use surface-sensitive mass spectrometry techniques and gas phase detection to study N-immobilization in soil and subsequent enhancements in reactivity that lead to decomposition of organic matter. The results will be used to reduce the uncertainty in projections from the Community Earth System Model (CESM) stemming from inaccurate representations of soil NO y emissions. The proposed research is significant because, in addition to demonstrating new mechanisms of NO y formation and loss, it will be a crucial first step towards modeling the land-atmosphere exchange of HONO and NO 2 in the CESM. Improved model treatment of land-air exchange of NO y is key for understanding feedbacks between human activity and climate, and addressing societal concerns about the fate of N and C emitted to the atmosphere.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Innovative Polyhydroxyalkanoates (PHA) Production with Microbial Electrochemical Technology (MET)

The project “Innovative Polyhydroxyalkanoates (PHA) Production with Microbial Electrochemical Technology (MET)” addressed food waste disposal challenges by successfully converting food waste to bioplastics (known as PHAs). The novel process created by our team of researchers from universities, national labs, and industry substantially enhanced overall carbon conversion efficiency of food waste processing (> 50%), while reducing disposal costs (> 25%). The project showed economic viability potential at community scale through pilot-scale demonstration at a relevant scale (50 L reactor volume) with more than 100 hours of PHA production using realistic conditions. The project goal was to valorize food waste by shunting traditional anaerobic digestion processing and creating a value-added PHA processing route that improves the economics and sustainability of local, community-scale, wet organic waste treatment. First, the food waste undergoes microbial-based, dark fermentation to break down the food to small carbon chains known as volatile fatty acids (VFAs). Instead of microorganisms converting the VFAs into methane using normal anaerobic digestion processing, our innovative process inhibits methane production. This preserves the produced VFAs for extraction and use by a novel Haloferax mediterranei (HM) archaea, which effectively converts the VFAs to bioplastics. The project added microbial electrochemical cells (MEC) to the dark fermentation process to enhance the VFAs produced and optimize the type of bioplastics formed.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Bringing Inorganic Carbon to Life: Developing Model Metalloenzymes for C1 Conversion Reactions

The global carbon cycle is carefully balanced through the use of specialized enzymes in plants, algae, bacteria, and archaea. A primordial metabolic pathway for the conversion of inorganic carbon into cellular biomass uses a large, nickel-containing enzyme called carbon monoxide dehydrogenase (CODH)/acetyl coenzyme A synthase (ACS). This system fixes carbon dioxide (CO 2 ) into carbon monoxide (CO) at the CODH site. The carbon monoxide is then used to generate acetyl coenzyme A, a biological building block, through a key carbon-carbon bond forming step at the nickel site in ACS. Despite the significance of these processes in the context of energy conversion, the fundamental chemistry underlying these transformations has remained elusive, in part due to the complexity of the natural enzyme. To better understand the principles governing these biological processes, which represent one-carbon (C 1 ) activation reactions, this project will develop functional models of CODH and ACS based on modifications to a small metalloprotein scaffold. Comprehensive characterization of these systems using advanced spectroscopic and biophysical techniques will reveal key elements responsible for conferring high levels of activity to the model systems, with implications for gaining insight into the mechanisms of the natural enzymes. Moreover, the principles learned from this research can be used to guide design of robust catalysts for efficient conversion of CO 2 and CO into liquid fuels.

10 SYNTHETIC FUELS↗
DOE OSTI2025

Mapping Nitrogen Pathways in Organic Manure through GCAM

As the world has become more and more globalized, a need for a comprehensive and extensive modelling system that maps out the vast majority of processes and items around the world and can display how interdependent they are. Furthermore, such a model should be able to predict future processes and values such that it can guide scientific thinking and policy. This is where the importance of GCAM becomes so apparent. GCAM, the Global Change Analysis Model, that incorporates many different fields and can predict such a wide variety of processes. As the model expands and encompasses more fields and goes into greater detail, there is a need for previously incorporated processes to be further fleshed out. My project is dedicated to creating the organic nitrogen fertilizer pathway, such that there are two nitrogen fertilizer pathways, synthetic and organic (manure). Previously, only synthetic fertilizer was included, with all organic fertilizer (manure) being omitted from the model. Developing the synthetic path is relatively easy, as the process for creating synthetic fertilizer is an industrial process that has been perfected over decades, and thus has a very precise input/output coefficient of nitrogen, but determining that same coefficient for organic manure is much harder, because, well, digestion is not an industrial process, especially considering the many different types of animals have different processes, and a good amount of the manure they produce won’t be applied to the soil. I obtained data from the UN’s FAO on manure nitrogen applied to soil, and filled in the gaps and created many different visualizations to help comprehend the data. These findings will foster a greater understanding of nitrogen flows, which is crucial to fields like industrial agriculture, polluting runoff, and nitrifying bacteria and archaea in the soil.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Engineering Microbial Communities: Frontier Science for the Bioeconomy Workshop Series

In nature, biological systems are shaped by complex interactions of diverse microorganisms such as bacteria, archaea, fungi, and viruses living within communities called microbiomes (Berg et al. 2020; Prescott 2017). These collective interactions result in emergent community properties that can be leveraged for beneficial purposes such as bioenergy and biomolecule production. Given this potential and the immensity of microbial genomic diversity, the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) program has long invested in research to better understand the biology of environmental microbes and microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and Conversion

Lignocellulosic plant biomass is a widely-abundant renewable resource that can be harnessed for value-added production of fuels & chemicals. While microbes have been engineered to breakdown lignocellulose and turn released sugars into products, this remains an energy-intensive process that requires expensive pre-treatment and separation steps. Furthermore, it is difficult to engineer all desirable traits for breakdown and conversion into one organism. This project developed a new strategy that relies on microbial partnerships formed in the herbivore rumen to liberate sugars from crude plant biomass and convert that sugar to value-added chemicals. Microbial consortia consisting of fungi, bacteria, and archaea form tight associations in the herbivore rumen, which divide-and-conquer the difficult tasks of biomass breakdown. This project leveraged a “synthetic rumen” consortium composed of anaerobic fungi and chain-elongating bacteria to study which metabolites are shared and exchanged between microbes and identify strategies to bolster lignocellulose conversion to value-added products. Our approach developed high-throughput systems and synthetic biology approaches to realize stable synthetic consortia that route lignocellulosic carbon into short and medium chain fatty acids (SCFAs/MCFAs) rather than methane. Key research objectives were to (1) design and predict anaerobic fungal and bacterial consortia that efficiently convert lignocellulosic biomass into medium-chain fatty acids (MCFAs), (2) understand how fermentation parameters and microbe-microbe interactions regulate and drive microbiome metabolic fluxes, and (3) use genomic editing to alter the fermentation byproducts of anaerobic fungi and bolster MCFA titers and yields.

09 BIOMASS FUELS↗
DOE OSTI2021

Genome Extraction from Shotgun Metagenome Sequence Data

Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only recently become possible. To realize the hope of capturing Earth’s microbial genetic complement, technologies that accelerate recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAG genomes, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq, and others. While portions of such capabilities are individually available from other resources, the combination of the intuitive usability, data interoperability, and integration of tools in a freely available compute resource makes KBase a uniquely powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended, with additional MAG recovery and analysis tools, via the KBase SDK (Software Development Kit).

Chivian, Dylan↗
DOE OSTI2020

A Genomic Catalogue of Earth’s Microbiomes - Introductory KBase Narrative

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled unprecedented insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this powerful approach to over 10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, human- and animal-host associated microbiomes, engineered environments, and natural and agricultural soils to capture extant microbial metabolic and functional potential. We present a comprehensive catalogue of 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units (OTUs), spanning 135 phyla, which expand the known phylogenetic diversity of Bacteria and Archaea by 44%. We also demonstrate the utility of this collection for secondary metabolite biosynthetic potential and predicting host-virus linkage, which can provide a view into the global distribution of lysogenic viruses. This resource underscores the value of leveraging genome-centric approaches to reveal genomic properties of uncultivated microbes that impact on ecosystem processes.

59 BASIC BIOLOGICAL SCIENCES↗