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At least 955 records · Page 53

Geologic hydrogen: From natural occurrences to anthropogenic generation – A review of fundamentals, potential, challenges and prospects

Growing demand for hydrogen is exposing the environmental and economic limits of reforming-based and carbon-managed supply chains, while the scale-up of electrolytic capacity remains capital-constrained. Geologic hydrogen, defined as molecular H₂ generated and stored within the Earth's crust offers a complementary, potentially lower-cost resource, yet exploration is still ad hoc. This review (1) revisits a global inventory of confirmed hydrogen seeps and subsurface occurrences; (2) analyzes the controlling reactions, migration pathways, and trapping conditions governing these occurrences; (3) proposes a process-based geologic hydrogen system concept analogous to, yet distinct from, the petroleum system; and (4) evaluates potential geologic hydrogen systems within the United States as a representative case study. Here, we contrast natural systems powered by serpentinization, mantle degassing or radiolysis with anthropogenic systems that stimulate the same reactions or convert in-situ hydrocarbons. Stable hydrogen accumulations require generation rates that outpace combined physical, chemical and microbial losses; the Bourakébougou field (Mali) exemplifies a self-recharging, free-gas reservoir sustained by meteoric-water serpentinization beneath an efficient caprock. Prospective geologic hydrogen resources are likely to occur in regions where iron-rich lithologies, deep-seated faults, and low-permeability sealing formations coexist. Applying this principle, we highlight three promising hydrogen play types in U.S. geological terrains: ophiolite belts (Appalachian and Californian regions), the Midcontinent Rift and the Lake Superior banded‑iron formations. Multiphysics numerical models and positive-unlabeled machine-learning workflows help to accelerate play screening and de-risk future production; yet, reaction kinetics, stimulation strategies, and full techno-economic and life-cycle assessments remain pivotal knowledge gaps.

Anthropogenic hydrogen generation↗

Combining organic amendments with enhanced rock weathering shifts soil carbon storage in croplands

Enhanced rock weathering (ERW) involves applying crushed silicate minerals to cropland soils to remove carbon dioxide and stabilize the global climate. If practiced widely, ERW has the potential to mitigate climate change and improve soil health and crop productivity. However, most ERW studies emphasize inorganic carbon (IC) chemistry, using model-based estimates and short-term mesocosms. Limited field data exist on how ERW interacts with organic amendments to affect organic carbon (C) cycling in soils. In a three-year field study in conventionally managed, irrigated maize fields, we monitored how key soil variables responded to crushed rock-alone, and in combination with compost and/or biochar. We measured weathering indicators (pH, major cations, and IC contents) and organic fractions, including particulate organic matter (POM), mineral-associated organic matter (MAOM), microbial biomass C, and water-extractable organic C. Rock-alone treatments increased weathering proxies (pH and IC) and showed an increasing trend in POM and MAOM, relative to control. In contrast, combining crushed rock with organic amendments resulted in lower soil organic C and nitrogen (N) concentrations (in both POM and MAOM) compared to organic amendments alone, though IC increased in the rock+compost treatment. Combining rock with both compost and biochar (compost/biochar) significantly lowered MAOM-N compared to compost/biochar alone. Overall, co-applying rock with organic inputs may promote weathering and C accrual but slow the accrual rate of organic C and N relative to organic amendments alone. Quantifying these trade-offs over multiple years and scales is critical to integrating ERW with existing soil health practices and climate mitigation strategies.

Biological and medical sciences↗

The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research

Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database, a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project’s interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team’s modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB’s expandability and flexible architecture allow it to serve as an example ecosystems database.

54 ENVIRONMENTAL SCIENCES↗

Microbial Communities in Microgravity: Simulation in Lab and on the Computer

Microorganisms grow differently in spaceflight than they do on Earth. While much remains unexplained about how microgravity affects microbial growth, one dominant hypothesis is that the lack of density-driven convection in the liquid growth environment makes mixing diffusion-limited, and therefore slower. This is supported by evidence that individual microbial strains experience starvation and acid stress in microgravity. However, if it is true, then microgravity would also have measurable effects on microbes in mixed communities, because many interspecies interactions involve the exchange of soluble metabolites through the medium (cross-feeding). Specifically, cooperative cross-feeding communities would grow more slowly in microgravity, and cooperation would be less stable on evolutionary timescales. Here we describe our efforts to test this hypothesis by simulating microgravity in silico and in the lab, using a model system of Eschericia coli and Salmonella enterica that grow only when they can exchange methionine and acetate. We created CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) as an extension of CFDEM®coupling software, to carry out computational modeling of biological flows, growth, and mass transfer in microgravity and also in laboratory artificial microgravity devices (rotating wall vessels, RWV). Using CAMDLES, we found distinct differences in growth rates between RWV and true microgravity, and we were able to identify several features, such as spatial distribution, biofilm formation, and product yield parameters, that influence the degree to which RWV growth recapitulates microgravity growth. In addition, we report on the development of a laboratory system for monitoring growth rates and species ratios of the community in RWVs, using fluorescent strains. Pairing CAMDLES with the laboratory model system allows us to generate quantitative predictions about the effects of spaceflight on organisms that will be essential to sustaining human space exploration in the long term.

microbiology↗

Vulnerability of mineral-organic associations in the rhizosphere

The majority of soil carbon (C) is stored in organic matter associated with reactive minerals. These mineral-organic associations (MOAs) inhibit microbial and enzymatic access to organic matter, suggesting that organic C within MOAs is resistant to decomposition. However, plant roots and rhizosphere microbes are known to transform minerals through dissolution and exchange reactions, implying that MOAs in the rhizosphere can be dynamic. Here we identify key drivers, mechanisms, and controls of MOA disruption in the rhizosphere and present a new conceptual framework for the vulnerability of soil C within MOAs. We introduce a vulnerability spectrum that highlights how MOAs characteristic of certain ecosystems are particularly susceptible to specific root-driven disruption mechanisms. This vulnerability spectrum provides a framework for critically assessing the importance of MOA disruption mechanisms at the ecosystem scale. Comprehensive representation of not only root-driven MOA formation, but also disruption, will improve model projections of soil C-climate feedbacks and guide the development of more effective soil C management strategies.

54 ENVIRONMENTAL SCIENCES↗

Organic sulfur from source to sink in low‐sulfate Lake Superior

Abstract Organic sulfur plays a crucial role in the biogeochemistry of aquatic sediments, especially in low sulfate (< 500 μ M) environments like freshwater lakes and the Earth's early oceans. To better understand organic sulfur cycling in these systems, we followed organic sulfur in the sulfate‐poor (< 40 μ M) iron‐rich (30–80 μ M) sediments of Lake Superior from source to sink. We identified microbial populations with shotgun metagenomic sequencing and characterized geochemical species in porewater and solid phases. In anoxic sediments, we found an active sulfur cycle fueled primarily by oxidized organic sulfur. Sediment incubations indicated a microbial capacity to hydrolyze sulfonates, sulfate esters, and sulfonic acids to sulfate. Gene abundances for dissimilatory sulfate reduction ( dsrAB ) increased with depth and coincided with sulfide maxima. Despite these indicators of sulfide formation, sulfide concentrations remain low (< 40 nM) due to both pyritization and organic matter sulfurization. Immediately below the oxycline, pyrite accounted for 13% of total sedimentary sulfur. Both free and intact lipids in this same interval accumulated disulfides, indicating rapid sulfurization even at low concentrations of sulfide. Our investigation revealed a new model of sulfur cycling in a low‐sulfate environment that likely extends to other modern lakes and possibly the ancient ocean, with organic sulfur both fueling sulfate reduction and consuming the resultant sulfide.

Phillips, Alexandra A.↗

Kinetic, metabolic, and statistical analytics: addressing metabolic transport limitations among organelles and microbial communities

Microbial organisms engage in a variety of metabolic interactions. A crucial part of these interactions is the exchange of molecules between different organelles, cells, and the environment. The main forces mediating this metabolic exchange are transporters. This transport can be difficult to measure experimentally because several transport mechanisms remain opaque. However, theoretical calculations about the inputs and outputs of cells via metabolic exchanges have enabled the successful inference of the workings of intra-organismal and inter-organismal systems. Kinetic, metabolic, and statistical modeling approaches in combination with omics data are enhancing our knowledge and understanding about metabolic exchange and mass resource allocation. Furthermore, this model-driven analytics approach can guide effective experimental design and yield new insights into biological function and control.

59 BASIC BIOLOGICAL SCIENCES↗

Progress Towards a New Model Chemolithoautotrophic Host (CRADA Final Report)

Some of the largest scale chemical processes for the production of important commodity chemicals and fuels involve an H 2 -containing gas mixture as an intermediate [e.g. ammonia, urea, methanol, Fischer-Tropsch (F-T) diesel, and hydrotreatment of crude petroleum to refined fuels]. The successful development of a model H 2 -oxidizing chemoautotrophic host could expand the range of fuels and chemicals produced from H 2 and CO 2 intermediates in the chemical, oil, and gas sectors in the near term, as well as from renewable and waste-derived sources of these gases that are expected to greatly expand in coming years. Among non-photosynthetic bacteria that can utilize H 2 and CO 2 , Cupriavidus necator (C. necator, formerly Ralstonia eutropha), is the best studied. C. necator is an excellent microbial host for the production of a variety of chemicals because it grows extremely quickly to very high cell densities autotrophically on H 2 and CO 2 , is genetically tractable, and has the ability to accumulate polymers, such as polyhydroxybutyrate, at industrial levels. Despite having great potential as a platform bioproduction host, genetic tools are limited, making metabolic engineering of this organism slow and laborious. In this CRADA project, we developed a number of genetic tools for C. necator: 1) Improvement of C. necator genetic transformation efficiency 2) Integration of heterologous genes into the C. necator chromosome and development of promoter library 3) Development of graded RBSs to control heterologous protein expression 4) Use of RBSs to demonstrate fatty alcohol production in C. necator 5) Demonstration of CRISPR-Cas9 gene editing in C. necator

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CFD Simulation of Aerobic Gas Fermentation to Enable Commercial Conversion of CO 2 into Aquaculture and Animal Feed: Cooperative Research and Development (Final Report)

NovoNutrients’ fermentation technology uses energy from hydrogen to transform industrial CO2 emissions into premium animal feed ingredients and other valuable products. A single NovoNutrients’ commercial manufacturing plant will capture and convert over 200,000 tons/yr of CO2 into over 100,000 tons/yr of high-protein feed. Key to the rapid and widespread deployment of the technology is maximization of its productivity and energy efficiency. Robust, physically based computational models of the technology will significantly increase productivity and efficiency, accelerating NovoNutrients’ technology to manufacturing scale. NREL has unique capabilities for creating and running such computational models. NREL's existing aerobic bioreaction computational fluid dynamics (CFD) models will be adapted to NovoNutrients’ gas fermentation (CO2, H2, O2) technology. The multiphysics CFD simulations require thousands of high-performance computing (HPC) node hours to simulate the complex geometries and contents of NovoNutrients’ industrial bioreactors. The experimentally validated CFD models were used to identify optimally efficient and productive bioreactor designs and operating conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microbial Pigments and Their Degradation Products as Biosignatures

Carotenoids are a class of vibrant biological pigments that have a characteristic chemical structure centered around a polyene core (Lu et al. 2018). Carotenoids and their derivatives are candidate biosignatures because they can persist in the terrestrial geologic record for up to 1.73 billion years (Vinnichenko et al. 2020), have specific structures that are likely the result of complex pathways, mediate the survival of many microorganisms in Mars and Ocean Worlds analog environments, and are detectable with multiple techniques, including Raman spectroscopy. In this project, we aim to investigate the detectability of carotenoid pigments with different spectroscopic methods to inform future instrument selection. We compare the spectra of five unaltered carotenoids, two model compounds, and carotenoid-forming archaeon with visible and deep UV Raman spectroscopy and UVVis absorption spectrophotometry. We then use one model pigment, beta-carotene, to evaluate the likelihood that unique spectral properties of carotenoids, or their refractory byproducts, would be preserved and detectable on a remote planetary surface by exposing it to simulated conditions for Mars. Sample Acquisition. Pigments betacarotene, lutein, zeaxanthin, astaxanthin, and lycopene were purchased from Sigma Aldrich. Halobacterium salinarum NRC-1 was acquired from Carlina Biological and grown in Halobacterium media. Mineral salts including sodium sulfate, sodium carbonate, and halite were used to form matrices in which the beta-carotene was embedded before exposure. Pigment-mineral mixes were at a 1:10 ratio in water. Analytical Techniques. Deep UV Raman data were collected on a custom laboratory mapping spectrometer called MOBIUS (Mineral and Organic Based Investigations using Ultraviolet Spectroscopy), which is an analog to the SHERLOC instrument on the Mars 2020 Perseverance rover (Bhartia et al. 2021). It features a 248.56 nm NeCu pulsed laser, liquid nitrogen-cooled detector, and tunable optical setup. Visible Raman data were collected using a Horiba Jobin Yvon LabRam HR spectrometer with a frequencydoubled Nd:YAG laser (532 nm) and a HeNe laser (633 nm). A VWR 6300 PC UV/Visible Spectrophotometer was used to collect absorption data for carotenoid solutions, model compounds, and solvents in UVpermissible capped cuvettes. Data were collected from 190-1100 nm at 1 nm increments. All spectral data were analyzed using Igor Pro 9 (Wavemetrics). Irradiation. We used a vacuum chamber equipped with a cryostat and a flood electron gun to simulate Martian surface temperatures, low pressures, and ionizing radiation (10keV, 10μA for 6h at 200K for our initial tests). The samples were prepared by drying the pigment-mineral mix onto polished metal tabs, then mounted on the cryostat for processing. Samples were then analyzed directly on the tabs after exposure. Results: In comparing the visible and deep UV Raman spectra of unaltered pigments, we found that they differed drastically. Carotenoids are often studied with visible Raman and typically have peaks at 1525 cm-1 and 1157 cm-1, due to the stretching of the C=C and C-C bonds in the polyene structure. However, in deep UV, the strongest feature is at ~1630 cm-1 and is broad, possibly indicating that multiple peaks are forming this feature. This stark difference is likely due to different preresonant enhancement effects. The UV-Vis results show that there is an absorption band in the deep UV <300 nm, which supports the hypothesis that the 248.6 nm excitation is interrogating another aspect of carotenoids than visible Raman. Our preliminary exposure tests indicated that pigments – even without minerals present - were largely unaltered in the applied conditions, with only a slight broadening in the primary polyene peaks apparent in the visible Raman data. Figure 1. A) Visible vs. deep UV Raman spectra of unaltered beta carotene. B) Schematic of exposure. Conclusions: Our results to date indicate that deep UV and visible Raman spectroscopy, both techniques with planetary mission heritage from Mars 2020 (Wiens et al. 2021, Bhartia et al. 2021), may be used in a complementary manner to observe carotenoids. In addition, we find that beta-carotene is largely resistant to our current exposure conditions, though there may be some amount of amorphization of the material which could cause the broadening of the peaks at 1525 and 1157 cm-1. As a next step, we aim to increase the dosage and duration of exposure to observe degradation of the parent pigment, possibly add UV as a factor via an Ar mini-arc UV lamp and use GC-MS to characterize possible degradation products.

pigments↗

Quantifying Membrane Structure and Dynamics during Bioproduct Production in Zymomonas mobilis by Molecular Simulation

The conversion of lignocellulosic biomass into biofuels and bioproducts by microbial biorefineries is central to a sustainable chemical industry. Zymomonas mobilis is one such biorefinery chassis and is resistant to ethanol stress, leading to its use in biomass conversion to biofuels and bioproducts. However, Z. mobilis growth is often inhibited by organic acids, aldehydes, alcohols, ketones, and amides found in biomass hydrolysate. The resulting slow growth inhibits production and as a result drives up the price for the resulting products. One hypothesis is that these molecules interact with or disrupt the bacterial membrane, triggering stress responses and hindering growth. To test this hypothesis at the molecular level, we employ all-atom molecular dynamics (MD) simulations to investigate lignocellulose-derived small molecules and their impact on a biologically relevant Z. mobilis membrane model. Simulations were conducted across a range of inhibitor concentrations from 0 to 2.5 mol %, analyzing key membrane properties such as area per lipid (APL), membrane thickness, lipid-order parameter (−S CH ), lateral diffusion coefficient (D xy ), and permeability coefficient (Pm). From simulation, we observed altered membrane structure and dynamics at these modest small molecule concentrations commonly found in hydrolysates. Generally, the membranes become thinner, with a higher area per lipid and lower-order parameter as the small molecule concentration increases. These trends are stronger for more hydrophobic molecules with greater hydrophobic bulk, as isobutanol, propanol, and propanoic acid showed greater membrane perturbations as the concentration increased compared to other small molecules. Tracking small molecule distributions directly in our equilibrium simulations allows us to determine concentration-dependent free energy profiles for these molecules. While the trends are noisy, generally the barriers to crossing the membrane decrease as the concentration increases, indicating that the membranes become leakier as small molecule concentrations rise. Comparing between native Z. mobilis membranes with hopanoids and membranes sharing the same phospholipid composition but without hopanoids, hopanoids stabilize and order the membrane for smaller molecules to maintain membrane structure but appear insufficient for larger hydrophobic molecules like isobutanol. These findings provide a mechanistic understanding of how small molecules found in biomass degradation streams interact with the Z. mobilis membrane, offering valuable insights for future strain engineering efforts to optimize biofuel and bioproduct synthesis from biomass feedstocks by highlighting limits to small molecule tolerance. This knowledge can guide the modification of membrane composition to develop more robust microbes, thereby improving microbial survival and yields in industrial contexts.

Singh, Nitin Kumar [Michigan State Univ., East Lan↗

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. In order to realize the hope of capturing Earth’s microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the 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/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, 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 available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a 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 software development kit (SDK).

59 BASIC BIOLOGICAL SCIENCES↗

Lignin conversion to β-ketoadipic acid by Pseudomonas putida via metabolic engineering and bioprocess development

Bioconversion of a heterogeneous mixture of lignin-related aromatic compounds (LRCs) to a single product via microbial biocatalysts is a promising approach to valorize lignin. Here, Pseudomonas putida KT2440 was engineered to convert mixed p-coumaroyl– and coniferyl-type LRCs to β-ketoadipic acid, a precursor for performance-advantaged polymers. Expression of enzymes mediating aromatic O-demethylation, hydroxylation, and ring-opening steps was tuned, and a global regulator was deleted. β-ketoadipate titers of 44.5 and 25 grams per liter and productivities of 1.15 and 0.66 grams per liter per hour were achieved from model LRCs and corn stover-derived LRCs, respectively, the latter representing an overall yield of 0.10 grams per gram corn stover-derived lignin. Technoeconomic analysis of the bioprocess and downstream processing predicted a β-ketoadipate minimum selling price of $\$2.01$ per kilogram, which is cost competitive with fossil carbon-derived adipic acid ($\$1.10$ to 1.80 per kilogram). Overall, this work achieved bioproduction metrics with economic relevance for conversion of lignin-derived streams into a performance-advantaged bioproduct.

09 BIOMASS FUELS↗

P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB)

Abstract Background The rnpB gene encodes for an essential catalytic RNA (RNase P). Like other essential RNAs, RNase P’s sequence is highly variable. However, unlike other essential RNAs (i.e. tRNA, 16 S, 6 S,...) its structure is also variable with at least 5 distinct structure types observed in prokaryotes. This structural variability makes it labor intensive and challenging to create and maintain covariance models for the detection of RNase P RNA in genomic and metagenomic sequences. The lack of a facile and rapid annotation algorithm has led to the rnpB gene being the most grossly under annotated essential gene in completed prokaryotic genomes with only a 24% annotation rate. Here we describe the coupling of the largest RNase P RNA database with the local alignment scoring algorithm to create the most sensitive and rapid prokaryote rnpB gene identification and annotation algorithm to date. Results Of the 2772 completed microbial genomes downloaded from GenBank only 665 genomes had an annotated rnpB gene. We applied P Finder to these genomes and were able to identify 2733 or nearly 99% of the 2772 microbial genomes examined. From these results four new rnpB genes that encode the minimal T-type P RNase P RNAs were identified computationally for the first time. In addition, only the second C-type RNase P RNA was identified in Sphaerobacter thermophilus . Of special note, no RNase P RNAs were detected in several obligate endosymbionts of sap sucking insects suggesting a novel evolutionary adaptation. Conclusions The coupling of the largest RNase P RNA database and associated structure class identification with the P Finder algorithm is both sensitive and rapid, yielding high quality results to aid researchers annotating either genomic or metagenomic data. It is the only algorithm to date that can identify challenging RNAse P classes such as C-type and the minimal T-type RNase P RNAs. P Finder is written in C# and has a user-friendly GUI that can run on multiple 64-bit windows platforms (Windows Vista/7/8/10). P Finder is free available for download at https://github.com/JChristopherEllis/P-Finder as well as a small sample RNase P RNA file for testing.

59 BASIC BIOLOGICAL SCIENCES↗

Using metacommunity ecology to understand environmental metabolomes

Abstract Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail.

54 ENVIRONMENTAL SCIENCES↗

Editorial for Special Issue “Advances in Soil Microbiome”

The soil microbiome (the community of all soil microorganisms and their surrounding environment) is a critical part of our ecological network. These microbial communities carry out several important functions, including the promotion of plant growth and the cycling of carbon and nitrogen sources. Despite the importance of this community, and the recent advances in multi-omic analysis and other methods designed to query complex systems, there is a still a large knowledge gap regarding the soil microbiome, its response to changing climates and moisture levels, the specific molecular mechanisms that drive its role in the environment, and how these questions can be answered through the use of model systems. Here, we present eleven new papers that seek to answer these questions and expand our knowledge of the soil microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

BONCAT-Live for isolation and cultivation of active environmental bacteria

In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.

Analytical Methods↗

High-throughput mapping of the phage resistance landscape in E. coli

Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.

59 BASIC BIOLOGICAL SCIENCES↗