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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Moab Desert Crust - Sample 4E

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 OSTI2022

Nramp: Deprive and conquer?

Solute carriers 11 (Slc11) evolved from bacterial permease (MntH) to eukaryotic antibacterial defense (Nramp) while continuously mediating proton (H+)-dependent manganese (Mn2+) import. Also, Nramp horizontal gene transfer (HGT) toward bacteria led to mntH polyphyly. Prior demonstration that evolutionary rate-shifts distinguishing Slc11 from outgroup carriers dictate catalytic specificity suggested that resolving Slc11 family tree may provide a function-aware phylogenetic framework. Hence, MntH C (MC) subgroups resulted from HGTs of prototype Nramp (pNs) parologs while archetype Nramp (aNs) correlated with phagocytosis. PHI-Blast based taxonomic profiling confirmed MntH B phylogroup is confined to anaerobic bacteria vs. MntH A (MA)’s broad distribution; suggested niche-related spread of MC subgroups; established that MA-variant MH, which carries ‘eukaryotic signature’ marks, predominates in archaea. Slc11 phylogeny shows MH is sister to Nramp. Site-specific analysis of Slc11 charge network known to interact with the protonmotive force demonstrates sequential rate-shifts that recapitulate Slc11 evolution. 3D mapping of similarly coevolved sites across Slc11 hydrophobic core revealed successive targeting of discrete areas. The data imply that pN HGT could advantage recipient bacteria for H+-dependent Mn2+ acquisition and Alphafold 3D models suggest conformational divergence among MC subgroups. It is proposed that Slc11 originated as a bacterial stress resistance function allowing Mn2+-dependent persistence in conditions adverse for growth, and that archaeal MH could contribute to eukaryogenesis as a Mn2+ sequestering defense perhaps favoring intracellular growth-competent bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Utility of Macroecological Rules for Microbial Biogeography

Macroecological rules have been developed for plants and animals that describe large-scale distributional patterns and attempt to explain the underlying physiological and ecological processes behind them. Similarly, microorganisms exhibit patterns in relative abundance, distribution, diversity, and traits across space and time, yet it remains unclear the extent to which microorganisms follow macroecological rules initially developed for macroorganisms. Additionally, the usefulness of these rules as a null hypothesis when surveying microorganisms has yet to be fully evaluated. With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. Here, we review and synthesize these macroecological microbial studies with two main objectives: (1) to determine to what extent macroecological rules explain the distribution of host-associated and free-living microorganisms, and (2) to understand which environmental factors and stochastic processes may explain these patterns among microbial clades (archaea, bacteria, fungi, and protists) and habitats (host-associated and free living; terrestrial and aquatic). Overall, 78% of microbial macroecology studies focused on free living, aquatic organisms. In addition, most studies examined macroecological rules at the community level with only 35% of studies surveying organismal patterns across space. At the community level microorganisms often tracked patterns of macroorganisms for island biogeography (74% confirm) but rarely followed Latitudinal Diversity Gradients (LDGs) of macroorganisms (only 32% confirm). However, when microorganisms and macroorganisms shared the same macroecological patterns, underlying environmental drivers (e.g., temperature) were the same. Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Chemotaxonomic patterns in intracellular metabolites of marine microbial plankton

Most biological diversity on Earth is contained within microbial communities. In the ocean, these communities dominate processes related to carbon fixation and nutrient recycling. Yet, specific factors that determine community composition and metabolic activity are difficult to resolve in complex microbial populations, complicating predictions of microbial processes in a changing ocean. Microbial metabolism generates small organic molecules that reflect both the biochemical and physiological diversity as well as the taxonomic specificity of these biological processes. These small molecules serve as the conduit for taxon-specific signaling and exchange. Here, we use liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to taxonomically categorize 111 metabolites that include small molecules in central and secondary metabolism across 42 taxa representing numerically dominant and metabolically important lineages of microbial autotrophs and heterotrophs. Patterns in metabolite presence-absence broadly reflected taxonomic lineages. A subset of metabolites that includes osmolytes, sulfur-containing metabolites, sugars, and amino acid derivatives provided chemotaxonomic information among phytoplankton taxa. A variety of phytohormones and signaling molecules were predominantly found in the heterotrophic bacteria and archaea, expanding knowledge of metabolites implicated in modulating interactions between microbes. This chemotaxonomic inventory of marine microbial metabolites is a key step in deciphering metabolic networks that influence ocean biogeochemical cycles.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

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

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

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Comparative Analysis of Microbial Diversity Across Temperature Gradients in Hot Springs From Yellowstone and Iceland

Geothermal hot springs are a natural setting to study microbial adaptation to a wide range of temperatures reaching up to boiling. Temperature gradients lead to distinct microbial communities that inhabit their optimum niches. We sampled three alkaline, high temperature (80–100°C) hot springs in Yellowstone and Iceland that had cooling outflows and whose microbial communities had not been studied previously. The microbial composition in sediments and mats was determined by DNA sequencing of rRNA gene amplicons. Over three dozen phyla of Archaea and Bacteria were identified, representing over 1700 distinct organisms. We observed a significant non-linear reduction in the number of microbial taxa as the temperature increased from warm (38°C) to boiling. At high taxonomic levels, the community structure was similar between the Yellowstone and Iceland hot springs. We identified potential endemism at the genus level, especially in thermophilic phototrophs, which may have been potentially driven by distinct environmental conditions and dispersal limitations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Novel Extracellular Electron Transfer Channels in a Gram-Positive Thermophilic Bacterium

Biogenic transformation of Fe minerals, associated with extracellular electron transfer (EET), allows microorganisms to exploit high-potential refractory electron acceptors for energy generation. EET-capable thermophiles are dominated by hyperthermophilic archaea and Gram-positive bacteria. Information on their EET pathways is sparse. Here, we describe EET channels in the thermophilic Gram-positive bacterium Carboxydothermus ferrireducens that drive exoelectrogenesis and rapid conversion of amorphous mineral ferrihydrite to large magnetite crystals. Microscopic studies indicated biocontrolled formation of unusual formicary-like ultrastructure of the magnetite crystals and revealed active colonization of anodes in bioelectrochemical systems (BESs) by C. ferrireducens . The internal structure of micron-scale biogenic magnetite crystals is reported for the first time. Genome analysis and expression profiling revealed three constitutive c -type multiheme cytochromes involved in electron exchange with ferrihydrite or an anode, sharing insignificant homology with previously described EET-related cytochromes thus representing novel determinants of EET. Our studies identify these cytochromes as extracellular and reveal potentially novel mechanisms of cell-to-mineral interactions in thermal environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Editorial: Microbial C1 Metabolism and Biotechnology

Archaea and bacteria with the capacity to utilize one-carbon (C1) molecules as carbon and energy sources are widespread across the planet and are important players in many biogeochemical processes. As such, they occupy an array of diverse anaerobic and aerobic niches and perform unique metabolisms that enable the utilization of carbon dioxide (CO 2 ), carbon monoxide (CO), formate (HCOOH), methanol (CH 3 OH), and methane (CH 4 ) for growth. Several industrial processes have been developed that leverage these microbes for the targeted conversion of anthropogenic waste gases that contain C1 molecules, including natural gas (CH 4 ), anaerobic digestion-derived biogas (CH 4 and CO 2 ), industrial flue gas (CO 2 and CO), and syngas (CO 2 , CO, and H 2 ) (Figure 1). Further, there is increasing interest in electrochemical reduction of CO 2 to CO, CH 4 , and intermediates with increased solubility compared to gaseous C1 molecules (formate and methanol) using electrons derived from renewable sources like wind, solar, or hydrothermal systems to mitigate atmospheric greenhouse gas. Thus, C1-utilizing microbes will likely play an integral role in biotechnologies that are part of a sustainable, circular bioeconomy. However, fundamental knowledge gaps into the metabolism and physiology of these microbes exist that limit their utility as biocatalysts for carbon-efficient biomanufacturing. This special topic presents studies focused on the fundamental aspects of C1 metabolism in diverse microbial systems with the ability to convert anthropogenic greenhouse gases into valuable products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Photoinhibition of comammox reaction in Nitrospira inopinata in a dose- and wavelength-dependent manner

Apparent contribution of complete ammonia-oxidizing organisms (comammox) to the global nitrogen cycle highlights the necessity for understanding niche differentiation of comammox bacteria among other ammonia oxidizers. While the high affinity for ammonia of the comammox species Nitrospira inopinata suggests their niche partitioning is expected to be centered in oligotrophic environments, their absence in nutrient-depleted environments (such as the oceans) suggests that other (abiotic) factors might control their distribution and spatial localization within microbial communities. Many ammonia- and nitrite-oxidizing organisms are sensitive to light; however, the photosensitivity of comammox has not been explored. Since comammox bacteria encode enzymatic machinery homologous to canonical ammonia-and nitrite-oxidizers, we hypothesized that comammox N. inopinata, the only available pure culture of this group of microorganisms, may be inhibited by illumination in a similar manner. We evaluated the impact of light intensity, wavelength, and duration on the degree of photoinhibition for cultures of the comammox species N. inopinata and the soil ammonia-oxidizing archaea Nitrososphaera viennensis. Both species were highly sensitive to light. Interestingly, mimicking diurnal light exposure caused an uncoupling of ammonia and nitrite oxidation in N. inopinata, indicating nitrite oxidation might be more sensitive to light exposure than ammonia oxidation. It is likely that light influences comammox spatial distribution in natural environments such as surface fresh waters according to diurnal cycles, light attenuation coefficients, and the light penetration depths. Our findings therefore provide ecophysiological insights for further studies on comammox both in field and laboratory settings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments

Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (∼0.5 cm) to deeper sediments (∼ 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.

16S rRNA gene amplicon↗
DOE OSTI2023

Biological methane production and accumulation under sulfate-rich conditions at Cape Lookout Bight, NC

Introduction: Anaerobic oxidation of methane (AOM) is hypothesized to occur through reverse hydrogenotrophic methanogenesis in marine sediments because sulfate reducers pull hydrogen concentrations so low that reverse hydrogenotrophic methanogenesis is exergonic. If true, hydrogenotrophic methanogenesis can theoretically co-occur with sulfate reduction if the organic matter is so labile that fermenters produce more hydrogen than sulfate reducers can consume, causing hydrogen concentrations to rise. Finding accumulation of biologically-produced methane in sulfate-containing organic-rich sediments would therefore support the theory that AOM occurs through reverse hydrogenotrophic methanogenesis since it would signal the absence of net AOM in the presence of sulfate. Methods: 16S rRNA gene libraries were compared to geochemistry and incubations in high depth-resolution sediment cores collected from organic-rich Cape Lookout Bight, North Carolina. Results: We found that methane began to accumulate while sulfate is still abundant (6–8 mM). Methane-cycling archaea ANME-1, Methanosarciniales, and Methanomicrobiales also increased at these depths. Incubations showed that methane production in the upper 16 cm in sulfate-rich sediments was biotic since it could be inhibited by 2-bromoethanosulfonoic acid (BES). Discussion: We conclude that methanogens mediate biological methane production in these organic-rich sediments at sulfate concentrations that inhibit methanogenesis in sediments with less labile organic matter, and that methane accumulation and growth of methanogens can occur under these conditions as well. Our data supports the theory that H2 concentrations, rather than the cooccurrence of sulfate and methane, control whether methanogenesis or AOM via reverse hydrogenotrophic methanogenesis occurs. We hypothesize that the high amount of labile organic matter at this site prevents AOM, allowing methane accumulation when sulfate is low but still present in mM concentrations

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Biochemical characterization of Fsa16295Glu from “Fervidibacter sacchari,” the first hyperthermophilic GH50 with β-1,3-endoglucanase activity and founding member of the subfamily GH50_3

The aerobic hyperthermophile “Fervidibacter sacchari” catabolizes diverse polysaccharides and is the only cultivated member of the class “Fervidibacteria” within the phylum Armatimonadota. It encodes 117 putative glycoside hydrolases (GHs), including two from GH family 50 (GH50). In this study, we expressed, purified, and functionally characterized one of these GH50 enzymes, Fsa16295Glu. We show that Fsa16295Glu is a β-1,3-endoglucanase with optimal activity on carboxymethyl curdlan (CM-curdlan) and only weak agarase activity, despite most GH50 enzymes being described as β-agarases. The purified enzyme has a wide temperature range of 4–95°C (optimal 80°C), making it the first characterized hyperthermophilic representative of GH50. The enzyme is also active at a broad pH range of at least 5.5–11 (optimal 6.5–10). Fsa16295Glu possesses a relatively high k cat /K M of 1.82 × 10 7 s-1 M-1 with CM-curdlan and degrades CM-curdlan nearly completely to sugar monomers, indicating preferential hydrolysis of glucans containing β-1,3 linkages. Finally, a phylogenetic analysis of Fsa16295Glu and all other GH50 enzymes revealed that Fsa16295Glu is distant from other characterized enzymes but phylogenetically related to enzymes from thermophilic archaea that were likely acquired horizontally from “Fervidibacteria.” Given its functional and phylogenetic novelty, we propose that Fsa16295Glu represents a new enzyme subfamily, GH50_3.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Bioindicator “fingerprints” of methane-emitting thermokarst features in Alaskan soils

Permafrost thaw increases the bioavailability of ancient organic matter, facilitating microbial metabolism of volatile organic compounds (VOCs), carbon dioxide, and methane (CH 4 ). The formation of thermokarst (thaw) lakes in icy, organic-rich Yedoma permafrost leads to high CH 4 emissions, and subsurface microbes that have the potential to be biogeochemical drivers of organic carbon turnover in these systems. However, to better characterize and quantify rates of permafrost changes, methods that further clarify the relationship between subsurface biogeochemical processes and microbial dynamics are needed. In this study, we investigated four sites (two well-drained thermokarst mounds, a drained thermokarst lake, and the terrestrial margin of a recently formed thermokarst lake) to determine whether biogenic VOCs (1) can be effectively collected during winter, and (2) whether winter sampling provides more biologically significant VOCs correlated with subsurface microbial metabolic potential. During the cold season (March 2023), we drilled boreholes at the four sites and collected cores to simultaneously characterize microbial populations and captured VOCs. VOC analysis of these sites revealed “fingerprints” that were distinct and unique to each site. Total VOCs from the boreholes included > 400 unique VOC features, including > 40 potentially biogenic VOCs related to microbial metabolism. Subsurface microbial community composition was distinct across sites; for example, methanogenic archaea were far more abundant at the thermokarst site characterized by high annual CH 4 emissions. The results obtained from this method strongly suggest that ∼10% of VOCs are potentially biogenic, and that biogenic VOCs can be mapped to subsurface microbial metabolisms. By better revealing the relationship between subsurface biogeochemical processes and microbial dynamics, this work advances our ability to monitor and predict subsurface carbon turnover in Arctic soils.

anaerobic degradation↗
DOE OSTI2021

A Two-Step PCR Protocol Enabling Flexible Primer Choice and High Sequencing Yield for Illumina MiSeq Meta-Barcoding

High-throughput amplicon sequencing that primarily targets the 16S ribosomal DNA (rDNA) (for bacteria and archaea) and the Internal Transcribed Spacer rDNA (for fungi) have facilitated microbial community discovery across diverse environments. A three-step PCR that utilizes flexible primer choices to construct the library for Illumina amplicon sequencing has been applied to several studies in forest and agricultural systems. The three-step PCR protocol, while producing high-quality reads, often yields a large number (up to 46%) of reads that are unable to be assigned to a specific sample according to its barcode. Here, we improve this technique through an optimized two-step PCR protocol. We tested and compared the improved two-step PCR meta-barcoding protocol against the three-step PCR protocol using four different primer pairs (fungal ITS: ITS1F-ITS2 and ITS1F-ITS4, and bacterial 16S: 515F-806R and 341F-806R). We demonstrate that the sequence quantity and recovery rate were significantly improved with the two-step PCR approach (fourfold more read counts per sample; determined reads ≈90% per run) while retaining high read quality (Q30 > 80%). Given that synthetic barcodes are incorporated independently from any specific primers, this two-step PCR protocol can be broadly adapted to different genomic regions and organisms of scientific interest.

16S rDNA↗
DOE OSTI2024

Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life

Topoisomerases regulate the topological state of cellular genomes to prevent impediments to vital cellular processes, including replication and transcription from suboptimal supercoiling of double-stranded DNA, and to untangle topological barriers generated as replication or recombination intermediates. The subfamily of type IA topoisomerases are the only topoisomerases that can alter the interlinking of both DNA and RNA. In this article, we provide a review of the mechanisms by which four highly conserved N-terminal protein domains fold into a toroidal structure, enabling cleavage and religation of a single strand of DNA or RNA. We also explore how these conserved domains can be combined with numerous non-conserved protein sequences located in the C-terminal domains to form a diverse range of type IA topoisomerases in Archaea, Bacteria, and Eukarya. There is at least one type IA topoisomerase present in nearly every free-living organism. The variation in C-terminal domain sequences and interacting partners such as helicases enable type IA topoisomerases to conduct important cellular functions that require the passage of nucleic acids through the break of a single-strand DNA or RNA that is held by the conserved N-terminal toroidal domains. In addition, this review will exam a range of human genetic disorders that have been linked to the malfunction of type IA topoisomerase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Effects of Metal and Metal Ion on Biomethane Productivity during Anaerobic Digestion of Dairy Manure

To overcome major limiting factors of microbial processes in anaerobic digestion (AD), metal and metal ions have been extensively studied. However, there is confusion about the effects of metals and metal ions on biomethane productivity in previous research. In this study, Zn and Zn 2+ were selected as representatives of metals and metal ions, respectively, to investigate the effects on biomethane productivity. After the metals and metal ions at different concentrations were added to the batch AD experiments under the same mesophilic conditions, a Zn dose of 1 g/L and a Zn 2+ dose of 4 mg/L were found to cause the highest biomethane production, respectively. The results indicate that metal (Zn) and metal ion (Zn 2+ ) have different mechanisms to improve AD performance. There may be two possible explanations. To act as conductive materials in interspecies electron transfer (IET), relatively high doses of metals (e.g., 1 g/L of Zn, 10 g/L of Fe) are needed to bridge the electron transfer from syntrophic bacteria to methanogenic archaea in the AD process. As essential mineral nutrients, the AD system requires relatively low doses of metal ions (e.g., 4 mg/L of Zn 2+ , 5 mg/L of Fe 2+ ) to supplement the component of various enzymes that catalyze anaerobic reactions and transformations. This research will provide clear insight for selecting appropriate amounts of metals or metal ions to enhance biomethane productivity for industrial AD processes.

09 BIOMASS FUELS↗
DOE OSTI2021

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data from: Nitrification is a minor source of nitrous oxide (N2O) in an agricultural landscape and declines with increasing management intensity

The long-term contribution of nitrification to nitrous oxide (N2O) emissions from terrestrial ecosystems is poorly known and thus poorly constrained in biogeochemical models. Here, using Bayesian inference to couple 25 years of in situ N2O flux measurements with site-specific Michaelis-Menten kinetics of nitrification-derived N2O, we test the relative importance of nitrification-derived N2O across six cropped and unmanaged ecosystems along a management intensity gradient in the U.S. Midwest. We found that the maximum potential contribution from nitrification to in situ N2O fluxes was 13-17% in a conventionally fertilized annual cropping system, 27-42% in a low-input cover-cropped annual cropping system, and 52-63% in perennial systems including a late successional deciduous forest. Actual values are likely to be less than 10% of these values because of low N2O yields in cultured nitrifiers (typically 0.04 to 8% of NH3 oxidized) and competing sinks for available NH4+ in situ. Most nitrification-derived N2O was produced by ammonia oxidizing bacteria (AOB) rather than archaea (AOA), who appeared responsible for no more than 30% of nitrification-derived N2O production in all but one ecosystem. Although the proportion of nitrification-derived N2O production was lowest in annual cropping systems, these ecosystems nevertheless produced more nitrification-derived N2O (higher Vmax) than perennial and successional ecosystems. We conclude that nitrification is minor relative to other sources of N2O in all ecosystems examined.

54 ENVIRONMENTAL SCIENCES↗