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Advancing river corridor science beyond disciplinary boundaries with an inductive approach to catalyse hypothesis generation

Abstract A unified conceptual framework for river corridors requires synthesis of diverse site‐, method‐ and discipline‐specific findings. The river research community has developed a substantial body of observations and process‐specific interpretations, but we are still lacking a comprehensive model to distill this knowledge into fundamental transferable concepts. We confront the challenge of how a discipline classically organized around the deductive model of systematically collecting of site‐, scale‐, and mechanism‐specific observations begins the process of synthesis. Machine learning is particularly well‐suited to inductive generation of hypotheses. In this study, we prototype an inductive approach to holistic synthesis of river corridor observations, using support vector machine regression to identify potential couplings or feedbacks that would not necessarily arise from classical approaches. This approach generated 672 relationships linking a suite of 157 variables each measured at 62 locations in a fifth order river network. Eighty four percent of these relationships have not been previously investigated, and representing potential (hypothetical) process connections. We document relationships consistent with current understanding including hydrologic exchange processes, microbial ecology, and the River Continuum Concept, supporting that the approach can identify meaningful relationships in the data. Moreover, we highlight examples of two novel research questions that stem from interpretation of inductively‐generated relationships. This study demonstrates the implementation of machine learning to sieve complex data sets and identify a small set of candidate relationships that warrant further study, including data types not commonly measured together. This structured approach complements traditional modes of inquiry, which are often limited by disciplinary perspectives and favour the careful pursuit of parsimony. Finally, we emphasize that this approach should be viewed as a complement to, rather than in place of, more traditional, deductive approaches to scientific discovery.

54 ENVIRONMENTAL SCIENCES↗

Consequences of Altered Root Nutrient Uptake for Soil Carbon Stabilization (Final Report)

Objectives: The primary objectives of this project are to improve our understanding of tropical forest belowground processes, and to increase representation of this biome in ecosystem-scale and global C cycle models. Belowground dynamics present a major source of uncertainty inhibiting our ability to predict C cycle responses to climate change. Representation of tropical forests in these models is particularly lacking, even though these ecosystems hold >25% of terrestrial C stocks. While the majority of humid tropical forests exist on relatively infertile soils (i.e. poor in rock-derived nutrients), enormous gradients in soil nutrient availability exist at landscape-scales due to shifts in geology and soil order. Soil fertility is likely to greatly influence how tropical soil C storage will respond to the declines in precipitation predicted for the tropics. In particular, root dynamics vary across soil fertility gradients, with roots representing the major input of C to subsurface soils. Root characteristics related to soil fertility include biomass, turnover, C exudates, tissue chemistry, and nutrient uptake rates, with each of these likely sensitive to changes in moisture. The proposed project will fully integrate field research with an existing ecosystem model to assess potential effects of drying on belowground tropical C dynamics across a range of soil fertilities. Project Description:. This project will identify key linkages among soil fertility, root nutrient uptake, root dynamics, and soil C storage. The hypothesized framework for understanding these linkages is: Tropical rainforest roots in relatively fertile soils have lesser root biomass, faster turnover, fewer exudates, and improved root tissue quality relative to infertile sites, all resulting from increased root nutrient uptake. Ultimately, these root characteristics in fertile soils promote proportionally greater long-term soil C storage in organo-mineral associations. Specifically, lower root exudates and improved root tissue quality in fertile soils reduce microbial respiration of extant soil C (i.e. “priming) and increase microbial C use efficiency, leading to sorption of protein-rich microbial and plant organic matter on soil mineral surfaces. However, the larger pools of mineral-associated C in fertile tropical soils are more vulnerable to decreased rainfall than smaller C pools in infertile soils, in part because of the lesser root biomass, faster turnover, and softer, more labile root tissues. Also, the shallower lateral rooting structures typical in fertile soils experience greater desiccation and death than deeper roots in infertile sites, with little short-term adaptation to drying.

54 ENVIRONMENTAL SCIENCES↗

Upland Yedoma taliks are an unpredicted source of atmospheric methane

Landscape drying associated with permafrost thaw is expected to enhance microbial methane oxidation in arctic soils. Here we show that ice-rich, Yedoma permafrost deposits, comprising a disproportionately large fraction of pan-arctic soil carbon, present an alternate trajectory. Field and laboratory observations indicate that talik (perennially thawed soils in permafrost) development in unsaturated Yedoma uplands leads to unexpectedly large methane emissions (35–78 mg m -2 d -1 summer, 150–180 mg m -2 d -1 winter). Upland Yedoma talik emissions were nearly three times higher annually than northern-wetland emissions on an areal basis. Approximately 70% emissions occurred in winter, when surface-soil freezing abated methanotrophy, enhancing methane escape from the talik. Remote sensing and numerical modeling indicate the potential for widespread upland talik formation across the pan-arctic Yedoma domain during the 21 st and 22 nd centuries. Contrary to current climate model predictions, these findings imply a positive and much larger permafrost-methane-climate feedback for upland Yedoma.

54 ENVIRONMENTAL SCIENCES↗

Simulation of anoxic lenses as exporters of reactivity in alluvial aquifer sediments

Sedimentary interfaces between contrasting hydrogeological facies in alluvial aquifers drive the development of biogeochemical interfaces that influence subsurface and surface water quality. Here, we calibrate a reactive transport model on a series of dual-domain column experiments, where centimeter-scale, low-permeability, organic-rich anoxic lenses are embedded in coarser-grained aquifer material. Simulations explicitly account for C, Fe, and S cycling at the interface between the lenses and the aquifer in water-saturated conditions. Our results highlight the role of fine-grained, organic-rich inclusions not only as sources or sinks for redox-sensitive species, but also as exporters of nutrients that stimulate downgradient biogeochemical cycling. By releasing large amounts of organic carbon into the surrounding aquifer, such lenses drive the development of proximal secondary reduction zones ("halos"), characterized by high microbial activity (e.g., sulfate reduction) and accumulation of reduced reaction products (e.g., iron sulfide). If similar secondary reduction zones develop within the hydraulically conductive domain of an aquifer, they would be highly susceptible to changes in hydrologic conditions, for instance oxygen pulses associated with seasonal snowmelt. Furthermore, our results also emphasize the limitations of relying solely on aqueous species measurements to inform reactivity in systems where fast redox cycling and/or sizeable particulate transport may limit the signature of reactivity in the dissolved phase.

54 ENVIRONMENTAL SCIENCES↗

Lactiplantibacillus plantarum 0111 Protects Against Influenza Virus by Modulating Intestinal Microbial-Mediated Immune Responses

There are some limitations of traditional influenza vaccines concerning novel mutant strains. Therefore, it is particularly important to develop preventive means for antigen-unrelated types of influenza viruses. Recent studies have shown that probiotics can modulate the immune system and reduce the severity of viral infections. In this study, we investigated the potential of Lactiplantibacillus plantarum 0111 against influenza virus H9N2. Challenge experiments showed that L. plantarum 0111 pretreatments could effectively improve mice’s survival rate and weight loss and reduce the inflammatory cytokines IL-6 and TNF-α in the lungs and bronchoalveolar lavage fluid (BALF) along with the degree of lung and intestinal injury. FMT experiment demonstrates that the protective effect produced by L. plantarum 0111 is associated with gut microorganisms. In addition, 16S high-throughput sequencing of the mouse intestinal microbiota showed that L. plantarum 0111 remodeled the intestinal microbiota after H9N2 infection and maintained the gut microbiota balance. In a mouse model, the oral administration of L. plantarum 0111 increased IFN-β expression in the serum and BALF. At the same time, the transcript levels of IFN-β and related ISGs in the intestine and lungs of mice were also increased. In addition, the activation and polarization of T cells in mesenteric lymph nodes (MLNs) and the spleen were detected by flow cytometry, and the results showed that L. plantarum 0111 modulated cytokines in T cells and increased IgA expression in B cells in the MLNs and spleen. Thus, L. plantarum 0111 may improve gut microbiota-mediated immune responses and thus, resist infection by the influenza virus, and it could be used as an effective preventive measure against the influenza virus.

Xing, Jun-Hong↗

2D reactive transport model of shale chemical weathering and biogeochemical fluxes along a mountainous hillslope, East River Watershed, Colorado: Input files and simulation results

This data package contains input files and simulation results for a two-dimensional (2D) reactive transport model used to quantitatively analyze the coupled hydrological and biogeochemical processes governing shale weathering and associated biogeochemical fluxes under realistic environmental conditions in the high-elevation East River Watershed. These data support the conclusions presented in Stolze et al. (Water Resources Research, under review), "Model-based interpretation of solute exports and carbon partitioning during shale weathering in a mountainous hillslope". The model simulates atmospheric-subsurface gas exchange, subsurface water flow, and shale weathering processes under dynamic, year-scale conditions along a shale-underlain hillslope located in the East River watershed. The simulations were performed using the PFLOTRAN flow and reactive transport code and executed on the Perlmutter supercomputer to leverage its large-scale parallel computing capabilities. The data package contains two zipped folders, "model_input_files" and "simulation_results", and one readme.txt file. "model_input_files" contains the necessary input files to run the calibrated base-base model presented in Stolze et al. (Water Resources Research, under review). "simulation_results" contains a single hdf5 file ("Output_2D_hillslope_model.h5") which includes the results of simulation performed using the base-case model. This file can be opened with HDFView 3.1.4, Python, or MATLAB. "readme.txt" contains relevant information about the base-case model and provides guidelines on how to run the associated input files provided in the folder "model_input_files". Furthermore, readme.txt provides information regarding the model results provided in "Output_2D_hillslope_model.h5" such as matrix dimensionality and output units. Field datasets used to evaluate model performance were collected at three monitoring wells located along a hillslope transect (PLM1, PLM2, and PLM3). Dissolved ion concentration data were collected from November 2016 to October 2021 for Ca, Mg, DIC, Na, K, SO4 (Dong et al., 2025 - dic_npoc_data_2014_2024.zip - DOI:10.15485/1660459; Williams et al., 2025 - anion_data_2014_2024.zip - DOI:10.15485/1668054; Dong et al., 2025 - cation_data_2014_2024.zip - DOI:10.15485/1668055). Note that we used the files named er_PLM1_xx_yy, er_PLM2_xx_yy, and er_PLM3_xx_yy where xx stands for the name of the aqueous species and yy stands for the depth where the measurements were performed. Soil water content ([0 - 1] m) and water table depth were collected from November 2016 to October 2021 (Wan et al., 2024 - Dynamic_water_table__depthsFig2b.csv and Soil_water_content_Fig4e.csv - DOI:10.15485/2322567). Gaseous CO2 concentration were collected from October 2020 to December 2021(Wan et al., 2024 - Soil_CO2_concentrations_Fig4h.csv - DOI:10.15485/2322567) Gaseous CO2 flux from the subsurface to the atmosphere were collected in the vicinity of PLM2 from October 2019 to May 2022 (Wu et al., 2025). Soil microbial biomass concentration was measured from August 2016 to June 2017 (Sorensen et al., 2019 - 2017_East_River_Pumphouse_Microbial_Biomass__1_.csv - DOI:10.15485/1577267) All field data are published as CSV files compatible with Microsoft Excel, MATLAB, and Python, or as text files. The coordinates of the monitoring wells and the CO2(g) flux sensor in the coordinate system WGS84 are: -PLM1: [38.9197710 ; -106.9492750] -PLM2: [38.9201580 ; -106.9487170] -PLM3: [38.9207843 ; -106.9483668] -PLM4: 38.9210060 ; -106.9479528] -CO2(g) flux sensor: [38.9199180 ; -106.9489906] ------------------------------------------------------------------------------------------- This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility using NERSC award BER-ERCAP 23980, BER-ERCAP 28550, and BER-ERCAP 33789.

54 ENVIRONMENTAL SCIENCES↗

Ectomycorrhizal Plant-Fungal Co-invasions as Natural Experiments for Connecting Plant and Fungal Traits to Their Ecosystem Consequences

Introductions and invasions by fungi, especially pathogens and mycorrhizal fungi, are widespread and potentially highly consequential for native ecosystems, but may also offer opportunities for linking microbial traits to their ecosystem functions. In particular, treating ectomycorrhizal (EM) invasions, i.e., co-invasions by EM fungi and their EM host plants, as natural experiments may offer a powerful approach for testing how microbial traits influence ecosystem functions. Forests dominated by EM symbiosis have unique biogeochemistry whereby the secretions of EM plants and fungi affect carbon (C) and nutrient cycling; moreover, particular lineages of EM fungi have unique functional traits. EM invasions may therefore alter the biogeochemistry of the native ecosystems they invade, especially nitrogen (N) and C cycling. By identifying “response traits” that favor the success of fungi in introductions and invasions (e.g., spore dispersal and germination) and their correlations with “effect traits” (e.g., nutrient-cycling enzymes) that can alter N and C cycling (and affect other coupled elemental cycles), one may be able to predict the functional consequences for ecosystems of fungal invasions using biogeochemistry models that incorporate fungal traits. Here, we review what is already known about how EM fungal community composition, traits, and ecosystem functions differ between native and exotic populations, focusing on the example of EM fungi associated with species of Pinus introduced from the Northern into the Southern Hemisphere. We develop hypotheses on how effects of introduced and invasive EM fungi may depend on interactions between soil N availability in the exotic range and EM fungal traits. We discuss how such hypotheses could be tested by utilizing Pinus introductions and invasions as a model system, especially when combined with controlled laboratory experiments. Finally, we illustrate how ecosystem modeling can be used to link fungal traits to their consequences for ecosystem N and C cycling in the context of biological invasions, and we highlight exciting avenues for future directions in understanding EM invasion.

59 BASIC BIOLOGICAL SCIENCES↗

Post-fire soil emissions of nitric oxide (NO) and nitrous oxide (N 2 O) across global ecosystems: a review

Wildfires may increase soil emissions of trace nitrogen (N) gases like nitric oxide (NO) and nitrous oxide (N 2 O) by changing soil physicochemical conditions and altering microbial processes like nitrification and denitrification. When 34 studies were synthesized, we found a significant increase in both NO and N 2 O emissions up to 1 year post-fire across studies spanning ecosystems globally. However, when fluxes were separated by ecosystem type, we found that individual ecosystem types responded uniquely to fire. Forest soils tended to emit more N 2 O after fire, but there was no significant effect on NO. Shrubland soils showed significant increases in both NO and N 2 O emissions after fires; often with extremely large but short-lived NO pulses occurring immediately after fire. Grassland NO emissions increased after fire, but the size of this effect was small relative to shrublands. N 2 O emissions from burned grasslands were highly variable with no significant effect. To better understand the variation in responses to fire across global ecosystems, more consistent measurements of variables recognized as important controls on soil fluxes of NO and N 2 O (e.g., N cycling rates, soil water content, pH, and substrate availability) are needed across studies. We also suggest that fire-specific elements like burn severity, microbial community succession, and the presence of char be considered by future studies. Our synthesis suggests that fires can exacerbate ecosystem N loss long after they burn, increasing soil emissions of NO and N 2 O with implications for ecosystem N loss, climate, and regional air quality as wildfires increase globally.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hypophosphite Is a Naturally Occurring Selective Inhibitor of Syntrophic Methanogenesis

Microbial methanogenesis is a major contributor to global warming, and methane fluxes represent a loss of energy and electrons from industrial ecosystems. The chemical space of methane control strategies is still underexplored. Most known methanogenesis inhibitors target methanogenic archaeal enzymes. However, interference with the exchange of syntrophic electron carriers (H 2 or formate) in methanogenic systems presents an additional target for methane control. Here, we show that hypophosphite (H 2 PO 2 − ), an inorganic formate analogue, is a potent and selective inhibitor of syntrophic methanogenesis versus primary fermentation in rice field sediments and cattle rumens. Hypophosphite is also generally recognized as safe and relatively nontoxic to plants and animals. Genetic screens and physiological assays in the model methanogen Methanococcus maripaludis S2 implicate formate metabolism as the target of hypophosphite inhibition. Currently, there is no known biological pathway for anaerobic hypophosphite oxidation, and hypophosphite is stable in anoxic sediments for weeks to months. Given its widespread natural occurrence, we propose that hypophosphite may modulate the carbon cycle in natural environments. Taken together, our results suggest that hypophosphite could be used as a safe, inexpensive strategy for methane control in syntrophic methanogenic ecosystems.

chemical inhibitor↗

The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge

Background: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. In this work, we hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. Results: We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch’s average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. Conclusion: Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales.

59 BASIC BIOLOGICAL SCIENCES↗

Novel Microbial Routes to Synthesize Industrially Significant Precursor Compounds

Ethylene is the most widely employed organic precursor compound in industry. The potential to impact ethylene formation via recently discovered microbial processes is tenable using plentiful CO2 feedstocks. The overall long-term objective of this project was to develop an industrially compatible microbial process to synthesize ethylene in high yields. The key objective of this project was to fully define and initially characterized a recently discovered and genetically regulated anaerobic pathway to produce high levels of ethylene called the Dihydroxyacetone Phosphate - Ethylene Pathway in phototrophic bacteria. This was addressed through the following specific aims: 1. Fully probe the catalytic potential of all enzymes of the DHAP ethylene pathway and determine the regulatory mechanism of DHAP-ethylene pathway gene expression. 2. Discover effective and active ethylene enzymes encoded in cultured and uncultured organisms from anoxic environments. 3.Model the thermodynamics and kinetics of ethylene synthetic pathways to guide engineering efforts in integrating best performing DHAP-ethylene pathway enzymes into model bacteria chassis for enhance ethylene yields. Through this project we discovered the initially missing genetic and enzyme component of the DHAP-ethylene pathway that directly synthesized ethylene and other important industrial compounds like methane and ethane from specific substrates. We uncovered and partially characterized a nitrogenase-like reductase that functions in DHAP-ethylene pathway specifically and in methionine synthesis in general. This nitrogenase-like system is called the Methylthio-Alkane Reductase (MAR) for its ability to cleave volatile organic sulfur compounds into methanethiol (CH3-SH) for methionine synthesis and a hydrocarbon byproduct. Key to the DHAP-ethylene pathway, MAR is the essential enzyme that cleaves 2-methylthioethanol (CH3-S-CH2-CH2-OH) into ethylene. Coordinately, we uncovered that the MAR genes and genes associated with conversion of methanethiol (CH3-SH) to methionine are under genetic control of a LysR Type Transcriptional Regulator called SalR, whose activity is dependent upon the amount of sulfate available to the cell. When sulfate as the preferred sulfur source for cell growth drops below 200 micromolar, SalR become active for expressing the MAR and methionine biosynthesis genes to enable the cell to grow from volatile organic sulfur compounds and make ethylene. Metabolic thermos-kinetic modeling revealed that these MAR reactions for ethylene and other hydrocarbon production are highly thermodynamically favorable and are one of the largest driving forces for ethylene production by the DHAP-ethylene pathway for high ethylene yields. Modeling also indicated that a key aldolase and to a lesser extent an isomerase of the DHAP-ethylene pathway for production of the ethylene precursor, 2-methylthioethanol, also would increase ethylene yields. Through metagenomic mining and gene synthesis by the JGI DNA synthesis program, over 500 aldolase and isomerase homologs were synthesized and screened. From this, variants were uncovered with substantially higher activity that increased ethylene yields 5-fold via the aldolase reaction and 1.5-fold via the isomerase reaction. Each of these elements that increase ethylene production were integrated together via plasmid under appropriate gene promoter elements in the phototrophic bacterium, Rhodospirillum rubrum, resulting in at least 3 orders of magnitude increase in ethylene yield from carbon dioxide feedstock.

10 SYNTHETIC FUELS↗

Uses of Multi-Objective Flux Analysis for Optimization of Microbial Production of Secondary Metabolites

Secondary metabolites are not essential for the growth of microorganisms, but they play a critical role in how microbes interact with their surroundings. In addition to this important ecological role, secondary metabolites also have a variety of agricultural, medicinal, and industrial uses, and thus the examination of secondary metabolism of plants and microbes is a growing scientific field. While the chemical production of certain secondary metabolites is possible, industrial-scale microbial production is a green and economically attractive alternative. This is even more true, given the advances in bioengineering that allow us to alter the workings of microbes in order to increase their production of compounds of interest. This type of engineering requires detailed knowledge of the “chassis” organism’s metabolism. Since the resources and the catalytic capacity of enzymes in microbes is finite, it is important to examine the tradeoffs between various bioprocesses in an engineered system and alter its working in a manner that minimally perturbs the robustness of the system while allowing for the maximum production of a product of interest. The in silico multi-objective analysis of metabolism using genome-scale models is an ideal method for such examinations.

59 BASIC BIOLOGICAL SCIENCES↗

On the Thermal Anomaly of Lake Untersee

Reported here is the outcome from a student internship undertaken with Dr. Chris McKay at the NASA Ames Research Center. The project for this internship focuses on Lake Untersee, an Earth analog for icy moons. The anoxic hole of Lake Untersee has a thermal bump that was first observed by Wand et al., 1997 and has been confirmed several times (Wand et al., 2006; Andersen 2011). The expected thermal profile of the hole is linear from 0 C at the thermocline to approximately 4 C, the ground temperature in Antarctica, at the bottom. Instead, there is an increase from 0 C near the thermocline to 5 C which is maintained for 7 m, then a linear profile to approximately 4 C near the bottom. Thermal modeling was conducted to quantify the energy input required to maintain the bump. The results revealed 2 sources. Chemical reactions and radiative energy were analyzed as possible explanation. The chemical analysis revealed a peak in Chlorophyll a at the same depth as the shallower source and several interesting reactions with maximum rates at the same location as the lower depth source. However, the energy released from these reactions was orders of magnitude smaller than required source. The radiation analysis revealed a profile with two peaks in similar locations to the sources and a total energy input within a factor of 1.5 of the required sources. The conclusion from this work is that photosynthesis and the chemical reactions support microbial life in the water column which in turn acts as an opacity to convert radiative energy into thermal energy. Recommendations for future work are aimed at quantifying the quantity and types of microbes present in the water column. Beyond the work of the project, two field trips are described and a discussion on benefits to the student of the internship is given.

Earth analog for icy moons↗

The effects of warming and soil chemistry on bacterial community structure in Arctic tundra soils

Soil microbial communities in the Arctic play a critical role in regulating the global carbon (C) cycle. Vast amounts of C are stored in northern latitude soils, and rising temperatures in the Arctic threaten to thaw permafrost, making relatively inaccessible C sources more available for mineralization by soil microbes. Few studies have characterized how microbial community structure responds to thawing permafrost in the context of varying soil chemistries associated with contrasting tundra landscapes. Here, we subjected active layer and permafrost soils from upland and lowland tundra sites on the North Slope of Alaska to a soil-warming incubation experiment and compared soil bacterial community profiles (obtained by 16S rRNA amplicon sequencing) before and after incubation. The influence of soil composition (characterized by mid-infrared [MIR] spectroscopy) on bacterial community structure and class abundance was analyzed using redundancy and correlation analyses. We found increased abundances of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes [Sphingobacteriia] post incubation, particularly in permafrost soils. The categorical descriptors site and soil layer had the most explanatory power in our predictive models of bacterial community structure, highlighting the close relationship between soil bacteria and the soil environment. Specific soil chemical attributes characterizing the soil environments that were found to be the best predictors include MIR spectral bands associated with inorganic C, silicates, amide II (C=N stretch), and carboxylics (C-O stretch), and MIR peak ratios representing C substrate quality. Overall, these results further characterize soil bacterial community shifts that may occur as a frozen environment with limited access to C sources, such as is found in undisturbed permafrost, transitions to warmer and more C-available environments, such as is predicted in thawing permafrost due to climate change.

16S rRNA sequencing↗

CeMbio - The Caenorhabditis elegans Microbiome Resource

The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.

59 BASIC BIOLOGICAL SCIENCES↗

H2 cycling and microbial bioenergetics in anoxic sediments

The simple biochemistry of H2 is central to a large number of microbial processes, affecting the interaction of organisms with each other and with the environment. In anoxic sediments, the great majority of microbial redox processes involve H2 as a reactant, product, or potential by-product, and the thermodynamics of these processes are thus highly sensitive to fluctuations in environmental H2 concentrations. In turn, H2 concentrations are controlled by the activity of H2-consuming microorganisms, which efficiently utilize this substrate down to levels which correspond to their bioenergetic limitations. Consequently, any environmental change which impacts the thermodynamics of H2-consuming organisms is mirrored by a corresponding change in H2 concentrations. This phenomenon is illustrated in anoxic sediments from Cape Lookout Bight, NC, USA: H2 concentrations are controlled by a suite of environmental parameters (e.g., temperature, sulfate concentrations) in a fashion which can be quantitatively described by a simple thermodynamic model. These findings allow us to calculate the apparent minimum quantity of biologically useful energy in situ. We find that sulfate reducing bacteria are not active at energy yields below -18 kJ per mole sulfate, while methanogenic archaea exhibit a minimum close to -10 kJ per mole methane.

Hoehler, Tori M.↗

Insight into the autoproteolysis mechanism of the RsgI9 anti‐σ factor from Clostridium thermocellum

Abstract Clostridium thermocellum is a potential microbial platform to convert abundant plant biomass to biofuels and other renewable chemicals. It efficiently degrades lignocellulosic biomass using a surface displayed cellulosome, a megadalton sized multienzyme containing complex. The enzymatic composition and architecture of the cellulosome is controlled by several transmembrane biomass‐sensing RsgI‐type anti‐σ factors. Recent studies suggest that these factors transduce signals from the cell surface via a conserved RsgI extracellular (CRE) domain (also called a periplasmic domain) that undergoes autoproteolysis through an incompletely understood mechanism. Here we report the structure of the autoproteolyzed CRE domain from the C. thermocellum RsgI9 anti‐σ factor, revealing that the cleaved fragments forming this domain associate to form a stable α/β/α sandwich fold. Based on AlphaFold2 modeling, molecular dynamics simulations, and tandem mass spectrometry, we propose that a conserved Asn‐Pro bond in RsgI9 autoproteolyzes via a succinimide intermediate whose formation is promoted by a conserved hydrogen bond network holding the scissile peptide bond in a strained conformation. As other RsgI anti‐σ factors share sequence homology to RsgI9, they likely autoproteolyze through a similar mechanism.

Takayesu, Allen↗

Microbial Characteristics of ISS Environmental Surfaces

The microbiome of environmental surfaces from the International Space Station were characterized in order to examine the relationship to crew and hardware maintenance. The Microbial Observatory (ISS-MO) experiment generated a microbial census of ISS environments using advanced molecular microbial community analyses along with traditional culture-based methods. Since the “omics” methodologies generated an extensive microbial census, significant insights into spaceflight-induced changes in the populations of beneficial and/or potentially harmful microbes were gained. Surface samples were collected from several ISS surface locations from three flight opportunities, and were returned to Earth via the Soyuz TMA-14M or the Space X Dragon capsule. In addition to cultivation methods, viable microbial burden, iTag-based sequencing, and metagenome analyses were carried out. The cultivable microbial bioburden differed by location and sampling event. Exploring the ISS environmental microbiome revealed presence of opportunistic pathogens and antibiotic resistant microbes. Genes involved in ATP binding cassette transporters, two component systems, and beta-lactam resistance were among a diverse set of metabolic and genetic information processing pathways. Whole genome sequencing (WGS) of 50 ISS strains exhibiting resistance to various antibiotics was carried out. The antibiotic resistant genes deduced from the WGS were compared with the resistomes generated directly from the gene pool of the environmental samples. Two unique Aspergillus fumigatus strains isolated from the ISS were characterized and compared to the experimentally established clinical isolates Af293 and CEA10. A virulence assessment in a neutrophil-deficient larval zebrafish model of invasive aspergillosis indicated that both ISSFT-021 and IF1SW-F4 were significantly more lethal compared to Af293 and CEA10. The findings from this Environmental “Omics” project should be exploited to enhance human health and well-being of a closed system. In other words, the ISS-MO research aims to "translate" findings in fundamental research into medical practice (pathogen detection) and meaningful health outcomes (countermeasure development).

Perry, Jay↗