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At least 1,099 records · Page 61

Nontronite and Montmorillonite as Nutrient Sources for Life on Mars

Clay minerals have been identified on Mars' oldest (Noachian) terrain and their presence suggests long-term water-rock interactions. The most commonly identified clay minerals on Mars to date are nontronite (Fe-smectite) and montmorillonite (Al-smectite) [1], both of which contain variable amounts of water both adsorbed on their surface and within their structural layers. Over Mars' history, these clay miner-al-water assemblages may have served as nutrient sources for microbial life.

Craig, P. I.↗

Unraveling plant–microbe symbioses using single-cell and spatial transcriptomics

Plant-microbe symbioses require intense interaction and genetic coordination to successfully establish in specific cell types of the host and symbiont. Traditional RNA-seq methodologies lack the cellular resolution to fully capture these complexities, but single-cell and spatial transcriptomics (ST) are now allowing scientists to probe symbiotic interactions at an unprecedented level of detail. Here, we discuss the advantages that novel spatial and single-cell transcriptomic technologies provide in studying plant-microbe endosymbioses and highlight key recent studies. Finally, we consider the remaining limitations of applying these approaches to symbiosis research, which are mainly related to the simultaneous capture of both plant and microbial transcripts within the same cells.

59 BASIC BIOLOGICAL SCIENCES↗

Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands

Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.

54 ENVIRONMENTAL SCIENCES↗

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

59 BASIC BIOLOGICAL SCIENCES↗

CPGminer: An Interactive Dashboard to Explore the Genomic Features and Taxonomy of Complete Prokaryotic Genomes

Prokaryotes, the earliest forms of life on Earth, play crucial roles in global biogeochemical processes in virtually all ecosystems. The ever-increasing amount of prokaryotic genome sequencing data provides a wealth of information to examine fundamental and applied questions through systematic genome comparison. Genomic features, such as genome size and GC content, and taxonomy-centric genomic features of complete prokaryotic genomes (CPGs) are crucial for various fields of microbial research and education, yet they are often overlooked. Additionally, creating systematically curated datasets that align with research concerns is an essential yet challenging task for wet-lab researchers. In this study, we introduce CPGminer, a user-friendly tool that allows researchers to quickly and easily examine the genomic features and taxonomy of CPGs and curate genome datasets. We also provide several examples to demonstrate its practical utility in addressing descriptive questions.

59 BASIC BIOLOGICAL SCIENCES↗

Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism

Synthetic microbial ecology has the potential to enhance the productivity and resiliency of biotechnology processes compared to approaches using single isolates. Engineering microbial consortia is challenging; however, one approach that has attracted significant attention is the creation of synthetic obligate mutualism using auxotrophic mutants that depend on each other for exchange or cross-feeding of metabolites. In this paper, we describe the integration of mutant library fitness profiling with mass spectrometry based exometabolomics as a method for constructing synthetic mutualism based on cross-feeding. Two industrially important species lacking known ecological interactions, Zymomonas mobilis and Escherichia coli, were selected as the test species. Amino acid exometabolites identified in the spent medium of Z. mobilis were used to select three corresponding E. coli auxotrophs (proA, pheA and IlvA), as potential E. coli counterparts for the coculture. A pooled mutant fitness assay with a Z. mobilis transposon mutant library was used to identify mutants with improved growth in the presence of E. coli. An auxotroph mutant in a gene (ZMO0748) with sequence similarity to cysteine synthase A (cysK), was selected as the Z. mobilis counterpart for the coculture. Exometabolomic analysis of spent E. coli medium identified glutathione related metabolites as potentially available for rescue of the Z. mobilis cysteine synthase mutant. Three sets of cocultures between the Z. mobilis auxotroph and each of the three E. coli auxotrophs were monitored by optical density for growth and analyzed by flow cytometry to confirm high cell counts for each species. Taken together, our methods provide a technological framework for creating synthetic mutualisms combining existing screening based methods and exometabolomics for both the selection of obligate mutualism partners and elucidation of metabolites involved in auxotroph rescue.

59 BASIC BIOLOGICAL SCIENCES↗

Composition and in situ structure of the Methanospirillum hungatei cell envelope and surface layer

Archaea share genomic similarities with Eukarya and cellular architectural similarities with Bacteria, though archaeal and bacterial surface layers (S-layers) differ. Using cellular cryo–electron tomography, we visualized the S-layer lattice surroundingMethanospirillum hungatei, a methanogenic archaeon. Though more compact than known structures,M. hungatei’s S-layer is a flexible hexagonal lattice of dome-shaped tiles, uniformly spaced from both the overlying cell sheath and the underlying cell membrane. Subtomogram averaging resolved the S-layer hexamer tile at 6.4-angstrom resolution. By fitting an AlphaFold model into hexamer tiles in flat and curved conformations, we uncover intra- and intertile interactions that contribute to the S-layer’s cylindrical and flexible architecture, along with a spacer extension for cell membrane attachment.M. hungateicell’s end plug structure, likely composed of S-layer isoforms, further highlights the uniqueness of this archaeal cell. These structural features offer advantages for methane release and reflect divergent evolutionary adaptations to environmental pressures during early microbial emergence.

Science & Technology - Other Topics↗

Quantifying the inhibitory impact of soluble phenolics on anaerobic carbon mineralization in a thawing permafrost peatland

The mechanisms controlling the extraordinarily slow carbon (C) mineralization rates characteristic of Sphagnum -rich peatlands (“bogs”) are not fully understood, despite decades of research on this topic. Soluble phenolic compounds have been invoked as potentially significant contributors to bog peat recalcitrance due to their affinity to slow microbial metabolism and cell growth. Despite this potentially significant role, the effects of soluble phenolic compounds on bog peat C mineralization remain unclear. We analyzed this effect by manipulating the concentration of free soluble phenolics in anaerobic bog and fen peat incubations using water-soluble polyvinylpyrrolidone (“PVP”), a compound that binds with and inactivates phenolics, preventing phenolic-enzyme interactions. CO 2 and CH 4 production rates (end-products of anaerobic C mineralization) generally correlated positively with PVP concentration following Michaelis-Menten (M.M.) saturation functions. Using M.M. parameters, we estimated that the extent to which phenolics inhibit anaerobic CO 2 production was significantly higher in the bog—62 ± 16%—than the fen—14 ± 4%. This difference was found to be more substantial with regards to methane production—wherein phenolic inhibition for the bog was estimated at 54 ± 19%, while the fen demonstrated no apparent inhibition. Consistent with this habitat difference, we observed significantly higher soluble phenolic content in bog vs. fen pore-water. Together, these findings suggest that soluble phenolics could contribute to bogs’ extraordinary recalcitrance and high (relative to other peatland habitats) CO 2 :CH 4 production ratios.

59 BASIC BIOLOGICAL SCIENCES↗

Exploring Mars for Evidence of Habitable Environments and Life

The climate of Mars has been more similar to that of Earth than has the climate of any other planet in our Solar System. But Mars still provides a valuable alternative example of how planetary processes and environments can affect the potential presence of life elsewhere. For example, although Mars also differentiated very early into a core, mantle and crust, it then evolved mostly if not completely without plate tectonics and has lost most of its early atmosphere. The Martian crust has been more stable than that of Earth, thus it has probably preserved a more complete record of its earliest history. Orbital observations determined that near-surface water was once pervasive. Orbiters have identified the following diverse aqueous sedimentary deposits: layered phyllosilicates, phyllosilicates in intracrater fans, plains sediments potentially harboring evaporitic minerals, deep phyllosilicates, carbonate-bearing deposits, intracrater clay-sulfate deposits, Meridiani-type layered deposits, valles-type layered deposits, hydrated silica-bearing deposits, and gypsum plains. These features, together with evidence of more vigorous past geologic activity, indicate that early climates were wetter and perhaps also somewhat warmer. The denser atmosphere that was required for liquid water to be stable on the surface also provided more substantial protection from radiation. Whereas ancient climates might have favored habitable environments at least in some localities, clearly much of the Martian surface for most of its history has been markedly less favorable for life. The combination of dry conditions, oxidizing surface environments and typically low rates of sedimentation are not conducive to the preservation of evidence of ancient environments and any biota. Thus a strategy is required whereby candidate sites are first identified and then characterized for their potential to preserve evidence of past habitable environments. Rovers are then sent to explore the most promising candidates. The Mars Exploration Rover (MER) Opportunity revealed that water once flowed to the surface across the vast Meridiani plains, creating saline lakes whose waters were roiled by ancient winds that also sculptured their salt deposits into sand dunes. Opportunity then drove more than 30 km to explore even older deposits on a crater rim. MER Spirit found evidence that thermal waters (heated by volcanism or by impacts?) altered rocks to create sulfate salts, and siliceous sinters. These discoveries indicate that an early hydrological cycle apparently sustained precipitation, streams and lakes. Liquid water participated in rock weathering reactions, such as iron and sulfur oxidation, that created distinctive weathering regimes. Volcanism, impacts, groundwater and ice interacted at least locally. Redox chemical energy from volcanism, hydrothermal activity and weathering of crustal materials would have been available for any life. Thus conditions might have supported life in the past, at least locally. The main objective of the Mars Science Laboratory (MSL) Curiosity rover is to determine the extent to which Gale crater hosted environments capable of supporting microbial life. The rover has already found stream gravels as well as sediments that might have been deposited in an ancient lake. The rover is now traversing to Mt. Sharp, a 5 km-high mound that is located on the crater floor and that exhibits layered sedimentary rocks having diverse minerals (sulfates and clays) that apparently formed in the presence of liquid water. This rock sequence was deposited over an extended time period in diverse potentially habitable watery environments. Curiosity is poised to characterize a a well-preserved rock record of hundreds of millions of years of diverse environments and profound climate change.

layered phyllosilicates↗

Warming Effects of Spring Rainfall Increase Methane Emissions From Thawing Permafrost

Methane emissions regulate the near-term global warming potential of permafrost thaw, particularly where loss of ice-rich permafrost converts forest and tundra into wetlands. Northern latitudes are expected to get warmer and wetter, and while there is consensus that warming will increase thaw and methane emissions, effects of increased precipitation are uncertain. At a thawing wetland complex in Interior Alaska, we found that interactions between rain and deep soil temperatures controlled methane emissions. In rainy years, recharge from the watershed rapidly altered wetland soil temperatures, warming the top ~80cm of soil in spring and summer and cooling it in autumn. When soils were warmed by spring rainfall, methane emissions increased by ~30%. The warm, deep soils early in the growing season likely supported both microbial and plant processes that enhanced emissions. Finally, our study identifies an important and unconsidered role of rain in governing the radiative forcing of thawing permafrost landscapes.

58 GEOSCIENCES↗

Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum

Significant hurdles exist in efforts to domesticate and industrialize a microbial species for biotechnological application as specific metabolic functions found in natural communities disappear in axenic cultures. For the lignocellulose-deconstructing specialist Clostridium thermocellum, the catabolism of hemicellulose-derived pentoses, which the bacterium cannot ferment, is one such function. Here, we report that various xylo-oligomers significantly inhibit C. thermocellum metabolism and growth and that microbe-sugar interactions occur across multiple dimensions. First, stable isotope metabolomics confirmed C. thermocellum s ability to transport and metabolize pentose sugars. This transport occurs, at least in part, through the ATP-dependent transporter, CbpD. Secondly, xylose is an electron sink for C. thermocellum metabolism leading to the production of xylitol. Deletion of Clo1313_0076, annotated as a xylitol dehydrogenase, reduced the total production and molar xylitol yields by 41% and 46%, respectively. However, it also altered the relative end-product distribution patterns confirming that external electron acceptors may influence the bacterium s redox metabolism to a greater extent than previously considered. Finally, xylose-induced inhibition corresponds with the up-regulation and biogenesis of an AgrD-type, lactone cyclized pentapeptide signaling molecule; which is the first report of an AgrD-type signaling peptide in any thermophile. Addition of synthetic versions of the cyclic peptide inhibited cultures grown in the absence of xylose, but had no effect on cultures already inhibited by the pentose sugar. Together, our findings identify that C. thermocellum has evolved previously unrecognized strategies to cope with C5-sugars, but the absence of a native catabolic sink negatively affects strain metabolism and growth.

59 BASIC BIOLOGICAL SCIENCES↗

Disentangling direct from indirect relationships in association networks

Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect interactions are pervasive in all types of networks. However, quantitatively disentangling direct and indirect relationships in networks remains a formidable task. Here, we present a framework, called iDIRECT (Inference of Direct and Indirect Relationships with Effective Copula-based Transitivity), for quantitatively inferring direct dependencies in association networks. Using copula-based transitivity, iDIRECT eliminates/ameliorates several challenging mathematical problems, including ill-conditioning, self-looping, and interaction strength overflow. With simulation data as benchmark examples, iDIRECT showed high prediction accuracies. Application of iDIRECT to reconstruct gene regulatory networks in Escherichia coli also revealed considerably higher prediction power than the best-performing approaches in the DREAM5 (Dialogue on Reverse Engineering Assessment and Methods project, #5) Network Inference Challenge. In addition, applying iDIRECT to highly diverse grassland soil microbial communities in response to climate warming showed that the iDIRECT-processed networks were significantly different from the original networks, with considerably fewer nodes, links, and connectivity, but higher relative modularity. Further analysis revealed that the iDIRECT-processed network was more complex under warming than the control and more robust to both random and target species removal ( P < 0.001). As a general approach, iDIRECT has great advantages for network inference, and it should be widely applicable to infer direct relationships in association networks across diverse disciplines in science and engineering.

59 BASIC BIOLOGICAL SCIENCES↗

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

IslandViewer is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer’s integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria

The bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains and in the context of complex bacterial communities. Quantitative methods that can resolve closely related bacteria within complex communities can lead to a better understanding of plant–microbe interactions. However, current methods often lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study duckweed–associated bacteria. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed–bacterium associations, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed–bacterium associations present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root–frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe associations within plant-microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

Hydrogenation of organic matter as a terminal electron sink sustains high CO 2 :CH 4 production ratios during anaerobic decomposition

Once inorganic electron acceptors are depleted, organic matter in anoxic environments decomposes by hydrolysis, fermentation, and methanogenesis, requiring syntrophic interactions between microorganisms to achieve energetic favorability. In this classic anaerobic food chain, methanogenesis represents the terminal electron accepting (TEA) process, ultimately producing equimolar CO2 and CH4 for each molecule of organic matter degraded. However, CO2:CH4 production in Sphagnum-derived, mineral-poor, cellulosic peat often substantially exceeds this 1:1 ratio, even in the absence of measureable inorganic TEAs. Since the oxidation state of C in both cellulose-derived organic matter and acetate is 0, and CO2 has an oxidation state of +4, if CH4 (oxidation state -4) is not produced in equal ratio, then some other compound(s) must balance CO2 production by receiving 4 electrons. Here we present evidence for ubiquitous hydrogenation of diverse unsaturated compounds that appear to serve as organic TEAs in peat, thereby providing the necessary electron balance to sustain CO2:CH4 >1. While organic electron acceptors have previously been proposed to drive microbial respiration of organic matter through the reversible reduction of quinone moieties, the hydrogenation mechanism that we propose, by contrast, reduces C-C double bonds in organic matter thereby serving as 1) a terminal electron sink, 2) a mechanism for degrading complex unsaturated organic molecules, 3) a potential mechanism to regenerate electron-accepting quinones, and, in some cases, 4) a means to alleviate the toxicity of unsaturated aromatic acids. This mechanism for CO2 generation without concomitant CH4 production has the potential to regulate the global warming potential of peatlands by elevating CO2:CH4 production ratios.

58 GEOSCIENCES↗

Integrating viruses into soil food web biogeochemistry

The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. Finally, we highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.

59 BASIC BIOLOGICAL SCIENCES↗

Extracellular electron transfer across bio-nano interfaces for CO 2 electroreduction

Acetogenic bacteria represent a class of organisms capable of converting reducing equivalents and carbon dioxide into products with carbon–carbon bonds. Materials-based bio-electrochemical approaches are attractive for supplying biological organisms directly with grid-supplied electrons to convert carbon dioxide to value-added chemicals. Carbon nanotube-modified biocathodes have emerged as promising candidates for microbial electrosynthesis with high yields of carbon product formation, but a fundamental understanding of extracellular charge transfer at this electrode-biofilm interface is still lacking. Here, we utilize solid-state interfaces between semiconducting single-walled carbon nanotubes (s-SWCNT) and a model acetogenic bacterium for mechanistic studies of electro-catalytic CO 2 conversion to acetate. Studies of bacteria/s-SWCNT interactions in a transistor-based device suggest direct extracellular electron transfer (EET) at the bio-nano interface. Deuterium isotope labeling experiments confirmed that the availability of electrochemically produced H 2 as a redox mediator does not limit the efficiency of EET and CO 2 electro-reduction for C. ljungdahlii biofilms, suggesting the primary reducing equivalents are the electrons delivered across the electrode/bacterium interface or involvement of biological redox mediators. Additional isotope labeling studies demonstrate high Faradaic efficiency for CO 2 electro-reduction at the SWCNT/bacterium interface. These results provide important information about EET across the bacterium/material interface in a model biocathode.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Designer biomass for next-generation biorefineries: leveraging recent insights into xylan structure and biosynthesis

Xylans are the most abundant noncellulosic polysaccharides in lignified secondary cell walls of woody dicots and in both primary and secondary cell walls of grasses. These polysaccharides, which comprise 20–35% of terrestrial biomass, present major challenges for the efficient microbial bioconversion of lignocellulosic feedstocks to fuels and other value-added products. Xylans play a significant role in the recalcitrance of biomass to degradation, and their bioconversion requires metabolic pathways that are distinct from those used to metabolize cellulose. In this review, we discuss the key differences in the structural features of xylans across diverse plant species, how these features affect their interactions with cellulose and lignin, and recent developments in understanding their biosynthesis. In particular, we focus on how the combined structural and biosynthetic knowledge can be used as a basis for biomass engineering aimed at developing crops that are better suited as feedstocks for the bioconversion industry.

Biotechnology & Applied Microbiology↗