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At least 127 records · Page 7

Synthetic microbial communities: Bridging research and application in second-generation bioenergy feedstock microbiomes

The sustainable production of purpose-grown bioenergy feedstocks is essential in transitioning away from fossil fuels. Synthetic communities (SynComs) are consortia of microorganisms that can be used as biological interventions to support objectives like plant growth and stress tolerance. This review examines the state of knowledge regarding microbiomes and SynComs of second-generation bioenergy feedstocks, focusing on the rhizosphere. We first provide an overview of second-generation feedstocks, including switchgrass (Panicum virgatum), miscanthus (Miscanthus × giganteus), sorghum (Sorghum spp.), sugarcane (Saccharum spp.), and poplar (Populus spp.), and summarize our current understanding of their plant-soil-microbiome ecology. We next discuss considerations in the objectives, design, and evaluation of SynComs to enhance feedstock production, and then critically review the literature around their use. Our literature analysis revealed that SynCom performance varied substantially between controlled pilot experiments and field trials, possibly due to system complexity that could not be fully considered in their design and pilot evaluation. We identified a gap in the use of SynComs to support the unique sustainability objectives of biofuel feedstock agriculture, presenting an opportunity to leverage these additional microbial traits in SynCom designs. Finally, we emphasize the importance of targeted research to identify the ecological principles that govern the assembly, activation, and persistence of microbes in the feedstock rhizosphere, thereby enhancing our capacity to manage microbiomes under diverse environmental conditions and ensure their functionality. Beyond biofuels, SynComs are a promising microbiome management strategy for crop production; however, an ecologically informed design and evaluation of SynComs are advised.

SynCom↗

Higher-order interaction effects among operating conditions and feedstocks shape reactor microbiomes and fatty acid production profiles

Arrested anaerobic digestion (AAD) offers a promising route for producing fatty acids (FAs) from organic residues, yet optimal conditions for selectively generating medium-chain fatty acids (MCFAs) remain poorly defined. Here, we systematically evaluated the main and interaction effects of pH (5, 7, 9), feedstock (food waste, manure), temperature (35 and 45 °C), and inoculum source on microbiome composition and FA production. Anaerobic digester sludge and a novel bison rumen inoculum were compared. Significant higher-order interactions among operating parameters governed FA profiles and microbiome structure. Butyric acid production was driven by a three-way interaction among pH, feedstock, and temperature (p < 0.001), with maximum concentrations achieved in food waste reactors at pH 5.0 and 35 °C (1.2 ± 0.1 g L −1 with sludge and 1.1 ± 0.3 g L −1 with rumen). MCFA production exhibited significant four-way interactions (p < 0.1 to p < 0.001). At 45 °C and pH 5.0, inoculum source tuned MCFA selectivity: sludge favored pentanoic acid (0.4 ± 0.1 g L −1 ), whereas rumen favored hexanoic and heptanoic acids (up to 0.4 ± 0.2 g L −1 ). Manure reactors produced < 0.2 g L −1 MCFAs under all conditions. Genera, including Megasphaera, Prevotella, and Lactobacillus, were associated with production of specific MCFAs. PICRUSt2-based pathway predictions were consistent with MCFA production patterns and suggested a potential role for lactic acid–driven chain elongation pathways. This study provides insights into how interacting operating conditions shape AAD microbiomes, their FA profiles, and advances the trajectory of research aimed at engineering robust and controllable microbiomes for waste valorization.

09 BIOMASS FUELS↗

Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes

Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning

Abstract Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly; however, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. Here, we characterized the rate and composition of bacteria dispersing into surface soil via three dispersal routes (from the air above the vegetation, from nearby vegetation and leaf litter near the soil surface, and from the bulk soil and litter below the top layer). We then quantified the impact of those routes on microbial community composition and functioning in the topmost litter layer. The bacterial dispersal rate onto the surface layer was low (7900 cells/cm2/day) relative to the abundance of the resident community. While bacteria dispersed through all three routes at the same rate, only dispersal from above and near the soil surface impacted microbiome composition, suggesting that the composition, not rate, of dispersal influenced community assembly. Dispersal also impacted microbiome functioning. When exposed to dispersal, leaf litter decomposed faster than when dispersal was excluded, although neither decomposition rate nor litter chemistry differed by route. Overall, we conclude that the dispersal routes transport distinct bacterial communities that differentially influence the composition of the surface soil microbiome.

59 BASIC BIOLOGICAL SCIENCES↗

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.

59 BASIC BIOLOGICAL SCIENCES↗

Wildfire-dependent changes in soil microbiome diversity and function

Abstract Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and rhizosphere processes. Wildfire season length, and the frequency and size of severe fires have increased owing to climate change. Fires affect ecosystem recovery and modify soil microbiomes and microbially mediated biogeochemical processes. To study wildfire-dependent changes in soil microbiomes, we characterized functional shifts in the soil microbiota (bacteria, fungi and viruses) across burn severity gradients (low, moderate and high severity) 1 yr post fire in coniferous forests in Colorado and Wyoming, USA. We found severity-dependent increases of Actinobacteria encoding genes for heat resistance, fast growth, and pyrogenic carbon utilization that might enhance post-fire survival. We report that increased burn severity led to the loss of ectomycorrhizal fungi and less tolerant microbial taxa. Viruses remained active in post-fire soils and probably influenced carbon cycling and biogeochemistry via turnover of biomass and ecosystem-relevant auxiliary metabolic genes. Our genome-resolved analyses link post-fire soil microbial taxonomy to functions and reveal the complexity of post-fire soil microbiome activity.

59 BASIC BIOLOGICAL SCIENCES↗

Diet outperforms microbial transplant to drive microbiome recovery in mice

A high-fat, low-fibre Western-style diet (WD) induces microbiome dysbiosis characterized by reduced taxonomic diversity and metabolic breadth, which in turn increases risk for a wide array of metabolic, immune and systemic pathologies. Recent work has established that WD can impair microbiome resilience to acute perturbations such as antibiotic treatment, although little is known about the mechanism of impairment and the specific consequences for the host of prolonged post-antibiotic dysbiosis. Here, in this study, we characterize the trajectory by which the gut microbiome recovers its taxonomic and functional profile after antibiotic treatment in mice on regular chow (RC) or WD, and find that only mice on RC undergo a rapid successional process of recovery. Metabolic modelling indicates that a RC diet promotes the development of syntrophic cross-feeding interactions, whereas in mice on WD, a dominant taxon monopolizes readily available resources without releasing syntrophic byproducts. Intervention experiments reveal that an appropriate dietary resource environment is both necessary and sufficient for rapid and robust microbiome recovery, whereas microbial transplant is neither. Furthermore, prolonged post-antibiotic dysbiosis in mice on WD renders them susceptible to infection by the intestinal pathogen Salmonella enterica serovar Typhimurium. Our data challenge widespread enthusiasm for faecal microbiota transplant (FMT) as a strategy to address dysbiosis, and demonstrate that specific dietary interventions are, at a minimum, an essential prerequisite for effective FMT, and may afford a safer, more natural and less invasive alternative.

Kennedy, M. S. [University of Chicago, IL (United ↗

Oral microbiome and mycobiome dynamics in cancer therapy-induced oral mucositis

Cancer therapy-induced oral mucositis is a frequent major oncological problem, secondary to cytotoxicity of chemo-radiation treatment. Oral mucositis commonly occurs 7–10 days after initiation of therapy; it is a dose-limiting side effect causing significant pain, eating difficulty, need for parenteral nutrition and a rise of infections. The pathobiology derives from complex interactions between the epithelial component, inflammation, and the oral microbiome. Our longitudinal study analysed the dynamics of the oral microbiome (bacteria and fungi) in nineteen patients undergoing chemo-radiation therapy for oral and oropharyngeal squamous cell carcinoma as compared to healthy volunteers. The microbiome was characterized in multiple oral sample types using rRNA and ITS sequence amplicons and followed the treatment regimens. Microbial taxonomic diversity and relative abundance may be correlated with disease state, type of treatment and responses. Identification of microbial-host interactions could lead to further therapeutic interventions of mucositis to re-establish normal flora and promote patients’ health. Data presented here could enhance, complement and diversify other studies that link microbiomes to oral disease, prophylactics, treatments, and outcome.

60 APPLIED LIFE SCIENCES↗

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations

The soil environment is constantly changing due to shifts in soil moisture, nutrient availability and other conditions. To contend with these changes, soil microorganisms have evolved a variety of ways to adapt to environmental perturbations, including regulation of gene expression. However, it is challenging to untangle the complex phenotypic response of the soil to environmental change, partly due to the absence of predictive modeling frameworks that can mechanistically link molecular-level changes in soil microorganisms to a community’s functional phenotypes (or metaphenome). Towards filling this gap, we performed a combined analysis of metabolic and gene co-expression networks to explore how the soil microbiome responded to changes in soil moisture and nutrient conditions and to determine which genes were expressed under a given condition. Our integrated modeling approach revealed previously unknown, but critically important aspects of the soil microbiomes’ response to environmental perturbations. Incorporation of metabolomic and transcriptomic data into metabolic reaction networks identified condition-specific signature genes that are uniquely associated with dry, wet, and glycine-amended conditions. A subsequent gene co-expression network analysis revealed that drought-associated genes occupied more central positions in a network model of the soil community, compared to the genes associated with wet, and glycine-amended conditions. These results indicate the occurrence of system-wide metabolic coordination when soil microbiomes cope with moisture or nutrient perturbations. Importantly, the approach that we demonstrate here to analyze large-scale multi-omics data from a natural soil environment is applicable to other microbiome systems for which multi-omics data are available.

54 ENVIRONMENTAL SCIENCES↗

Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics

The human gut microbiome produces a complex mixture of biomolecules that interact with human physiology and play essential roles in health and disease. Crosstalk between micro-organisms and host cells is enabled by different direct contacts, but also by the export of molecules through secretion systems and extracellular vesicles. The resulting molecular network, comprised of various biomolecular moieties, has so far eluded systematic study. Here we present a methodological framework, optimized for the extraction of the microbiome-derived, extracellular biomolecular complement, including nucleic acids, (poly)peptides, and metabolites, from flash-frozen stool samples of healthy human individuals. Our method allows simultaneous isolation of individual biomolecular fractions from the same original stool sample, followed by specialized omic analyses. The resulting multi-omics data enable coherent data integration for the systematic characterization of this molecular complex. Our results demonstrate the distinctiveness of the different extracellular biomolecular fractions, both in terms of their taxonomic and functional composition. This highlights the challenge of inferring the extracellular biomolecular complement of the gut microbiome based on single-omic data. The developed methodological framework provides the foundation for systematically investigating mechanistic links between microbiome-secreted molecules, including those that are typically vesicle-associated, and their impact on host physiology in health and disease.

59 BASIC BIOLOGICAL SCIENCES↗

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗

Supplemental selenium source on gut health: insights on fecal microbiome and fermentation products of growing puppies

ABSTRACT Selenium is an essential trace element that can modulate the gut microbiome with an impact on host health. The present study aimed to evaluate the effects of organic (selenium-enriched yeast) vs inorganic (sodium selenite) selenium source on fecal end-fermentation products and gut microbiome of puppies from 20 to 52 weeks of age. Alpha and beta diversity of the gut bacterial community were affected by age but not by gender or selenium source. The relative abundance of taxa was differently affected by age, and the DNA concentration of all selected bacterial groups increased with age, although total volatile fatty acids (VFA), acetate, propionate, caproate and lactate concentrations decreased. Organic selenium was associated with a higher concentration of total VFA, propionate and butyrate, a higher number of DNA copies of Lactobacillus, and a trend to lower DNA copies of Escherichia coli. Effects on fecal microbiome during growth differed with selenium source. Females had higher fecal end-fermentation products related to protein degradation, whereas males had higher DNA concentration of Bifidobacterium. Organic selenium might be beneficial over inorganic for dog food supplementation due to the positive modulation of the gut microbiome observed in puppies.

Pereira, Ana Margarida↗

Microbiome Comparison and Pathogen Identification for Three Migrating Passerines Captured During Spring Season in Jordan Using 16S rRNA Sequencing

Jordan is located on an important spot along the Mediterranean and Black Sea Flyway. Hundreds of migratory bird species have been identified stopping over in Jordan during spring and autumn migratory seasons. Compared to mammals and economically important birds, the microbiomes of wild bird species are severely understudied. Gut microbial composition is a valuable source of information that reflects food preferences, foraging behavior, and the risk of pathogen transmission to humans and other animals. In this study, we assessed the microbiome composition of three species of migrating passerines (willow warblers, lesser whitethroats, and common reed warblers) captured during the spring migration stopover in Jordan in 2023. A total of 59 fecal samples were selected evenly from the three species and subjected to 16S sequencing and microbiome analysis. Our objectives were to determine the diversity of bacteria in these three species, assess the amount of intra- and inter-specific variation, and detect pathogenic genera and species that could pose health risks to humans, domestic animals, and wildlife. Bacteria mainly belonged to the phyla Proteobacteria (62%), Actinobacteriota (18%), Firmicutes (13%), Cyanobacteria (5%), and Bacteroidota (1%). The results reveal that lesser whitethroats had the greatest variation in bacterial genus richness, Shannon diversity, and microbial composition compared to willow warblers and common reed warblers. The three bird species harbored several pathogenic genera and species, including Campylobacter, Enterococcus, Escherichia-Shigella, Mycoplasma, Rickettsia, Clostridium perfringens, and Vibrio cholerae. We suggest further investigation to understand the relationship between migratory behavior and their gut microbiome. We advocate for the use of advanced molecular techniques to characterize the pathogens found in migratory birds that might have public and environmental health impacts in addition to economic loss.

59 BASIC BIOLOGICAL SCIENCES↗

Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion

Abstract Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning—the combustion of logging residue on the forest floor—is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.

Nelson, Amelia R.↗

Chronic drought differentially alters the belowground microbiome of drought tolerant and drought susceptible genotypes of Populus trichocarpa

Populus trichocarpa is an ecologically important tree species and economically important biofeedstock. Belowground, P. trichocarpa interacts with diverse microorganisms in the rhizosphere and root endosphere. These plant-microbial interactions can bolster a variety of plant processes, ranging from pathogen suppression to drought tolerance, yet we know little about the impact of chronic drought stress on P. trichocarpa’s belowground microbiomes. To investigate the interactive effect of chronic drought on belowground microbial communities across genetically different P. trichocarpa hosts, we assessed archaeal/bacterial and fungal communities within the root endosphere, rhizosphere, and surrounding bulk soil of selected genotypes in a long-term drought experiment in Boardman, OR, USA. We sequenced the 16S rRNA and ITS2 gene region on samples collected from 16 distinct P. trichocarpa genotypes in plots with full or reduced irrigation. Eight of these genotypes have been previously identified as drought tolerant while the other eight genotypes were drought susceptible. While reduced irrigation influenced the composition of every archaeal/bacterial microbiome compartment, fungal communities were only affected in the rhizosphere and bulk soil compartments. Drought-tolerant bacteria, such as Actinobacteria, were differentially abundant in reduced irrigation across all belowground microbiomes. Host drought-tolerance influenced plant-associated microbiome compartments but had little impact on the bulk soil compartment. Drought-tolerant trees were enriched for potential growth-promoting microorganisms in the root endosphere and rhizosphere, including Sphingomonas bacteria and ectomycorrhizal fungi. Overall, associations of growth-promoting microbes in drought resistant P. trichocarpa genotypes can be leveraged to improve biofeedstock productivity in regions prone to periodic drought.

59 BASIC BIOLOGICAL SCIENCES↗

Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables

Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host–associated and engineered systems. Notably, in spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population–level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week–over–week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage–associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re–examined in the context of ecological history and microbiome responses.

59 BASIC BIOLOGICAL SCIENCES↗

Summer thaw duration is a strong predictor of the soil microbiome and its response to permafrost thaw in arctic tundra

Abstract Climate warming has increased permafrost thaw in arctic tundra and extended the duration of annual thaw (number of thaw days in summer) along soil profiles. Predicting the microbial response to permafrost thaw depends largely on knowing how increased thaw duration affects the composition of the soil microbiome. Here, we determined soil microbiome composition from the annually thawed surface active layer down through permafrost from two tundra types at each of three sites on the North Slope of Alaska, USA. Variations in soil microbial taxa were found between sites up to ~90 km apart, between tundra types, and between soil depths. Microbiome differences at a site were greatest across transitions from thawed to permafrost depths. Results from correlation analysis based on multi‐decadal thaw surveys show that differences in thaw duration by depth were significantly, positively correlated with the abundance of dominant taxa in the active layer and negatively correlated with dominant taxa in the permafrost. Microbiome composition within the transition zone was statistically similar to that in the permafrost, indicating that recent decades of intermittent thaw have not yet induced a shift from permafrost to active‐layer microbes. We suggest that thaw duration rather than thaw frequency has a greater impact on the composition of microbial taxa within arctic soils.

54 ENVIRONMENTAL SCIENCES↗

Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes

Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change. IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.

Kellom, Matthew↗