Synthetic Community Research Articles

Wheat fungal endophyte communities are inseparable from the host and influence plant development.

Plants harbor complex and highly diverse fungal endophyte communities (FECs), making it difficult to evaluate the functional role of individual taxa, subsets of the community, or the FEC as a whole. To reduce the complexity of this system, we aimed to produce fungi-null wheat (Triticum aestivum) plants. To this end, we treated seeds with heat and fungicides and generated plants from rescued embryos and callus tissue. A culture-based approach and reverse transcription PCR analysis were negative, indicating that all treatments produced plants apparently free of fungi. However, the analysis of DNA using digital droplet PCR and next-generation sequencing revealed that tissues from all treatments retained low levels but diversity-rich FECs. While the FECs varied in composition across treatments and tissues, they all included core taxa of the mycobiome. The reduced fungal biomass, along with the changes in FEC composition, negatively affected plant development, supporting a FEC contribution to proper plant development and fitness. Our discovery that a large part of the FEC cannot be separated from plants and can be transmitted through seeds and tissue culture calls for reevaluation of particular microbiome paradigms, such as core taxa concepts, transmission modes, and functional species.IMPORTANCEThe native microbiome in a given plant must be considered when evaluating the effect of a single taxon or synthetic community. The pre-existing microbiome can interact with artificially added microbial cargo, which affects the final outcome. Such issues can be at least partially solved by the use of endophyte-free plants, which provide a clean background that should be useful in determining the effect of a single taxon, taxa combinations, or the entire microbiome on plant performance. Previous reports regarded plants as endophyte-free or axenic by the lack of fungal growth on culture media or the generation of plants from tissue cultures. We showed here that while fungi could not be isolated from fungicide-treated or tissue culture-regenerated plants, nevertheless, all plants contained rich fungal endophyte communities; namely, it was impossible to create fungi-free wheat plants. Our results call for rethinking fundamental microbiome-related concepts, such as core taxa, transmission mode, and functional species.

Syntrophy between bacteria and archaea enhances methane production in an EGSB bioreactor fed by cheese whey wastewater

The cheese-making process generates large amounts of cheese whey wastewater (CWW), which is abundant in nutrients but difficult to dispose of, contributing to the eutrophication of natural environments due to inadequate waste management. Here we show the anaerobic digestion of CCW by syntrophy between bacteria and archaea in an expanded granular sludge bed (EGSB) bioreactor as a low-cost alternative for bioremediation and biofuel production. The performance of the EGSB bioreactor and the composition of the natural microbial community were evaluated. During the operation of the EGSB bioreactor, physicochemical parameters such as alkalinity ratio (0.25), pH (7.5), and temperature (26°C) were attained and maintained, as well as light- and oxygen-free conditions, which favored the metabolism of oxygen-sensitive bacteria and methane-producing archaea (methanogens). Under these conditions, the chemical oxygen demand (COD) removal rate was highly efficient (> 89%). Methane (CH4) was produced from organic matter degradation by a few methanogens, mainly from Methanosaeta spp., and was enhanced by the metabolic interaction between bacteria and archaea. The biochemical methane potential (BMP) was >335 mL CH4/gCOD, indicating that the syntrophic microbial community is very efficient in removing organic matter and CH4 produced from CWW. Our results suggest that CWW could be treated in EGSB bioreactors and used as a sustainable alternative to CH4 production and also provide insights for the design of synthetic microbial communities (SynComs) for bioremediation, biogas production, and other biotechnological processes.

Synthetic Chemistry and Microelectrode Arrays: Building Stable Platforms for Point of Care Diagnostics

Molecular diagnostics typically require three main components. A molecular interaction that identifies a specific target, a device that detects, quantifies, and records that interaction, and an interface between the two. The interface is critical because it provides a means to fix molecular recognition elements to the surface of the device. For a "point-of-care" application, the interface must be stable both in terms of chemistry and time while still allowing the signal from the molecular interaction to be sensed and recorded by the device. For the use of a microelectrode array as the detection device, construction of the interface must also allow for individual molecular recognition elements to be placed by individual, addressable electrodes in the array.Because of the need for stability and synthetic flexibility, we made the choice to move away from the use of self-assembled monolayers as the interface for developing microelectrode arrays as point-of-care devices. To that end, we have employed diblock copolymers to coat the surface of microelectrode arrays, a change that has offered increased stability of the surface and enabled the use of a broad array of synthetic methods for functionalizing the electrodes in the array. In this talk, we show how the use of a diblock copolymer in conjunction with Cu(I)- and Cu(II)-mediated reactions can be used to functionalize a microelectrode array with multiple DNA-aptamers for the multiplex detection of metabolites. The resulting surface is stable for over 30 weeks (and counting), allows for the detection of multiple metabolites in the same experiment, and retains the detection sensitivity obtained with a self-assembled monolayer.One of the goals of the talk will also be to illustrate for the synthetic community the role that it can play in developing new tools for molecular diagnostics. After all, it is the surface on a microelectrode array that in the long-run defines what an array can be used for and the quality of the resulting analytical experiments. The construction of those surfaces is a synthetic chemistry challenge that moving forward will require both new synthetic methods and new approaches for characterization of the products generated from the new methods. One approach for characterization will be discussed in the context of the Cu(I)- and Cu(II)-mediated reactions employed in the current study.

Nutrient status changes bacterial interactions in a synthetic community.

Microbial interactions affect community stability and niche spaces in all ecosystems. However, it is not clear what factors influence these interactions, leading to changes in species fitness and ecological niches. Here, we utilized 16 monocultures and their corresponding pairwise co-cultures to measure niche changes among 16 cultivable bacterial species in a wide range of carbon sources, and we used resource availability as a parameter to alter the interactions of the synthetic bacterial community. Our results suggest that metabolic similarity drives niche deformation between bacterial species. We further found that resource limitation resulted in increased microbial inhibition and more negative interactions. At high resource availability, bacteria exhibited little inhibitory potential and stronger facilitation (in 71% of cases), promoting niche expansion. Overall, our results show that metabolic similarity induces different degrees of resource competition, altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. This framework may lay the basis for understanding complex niche deformation and microbial interactions as modulated by metabolic similarity and resource availability.IMPORTANCEUnderstanding the intricate dynamics of microbial interactions is crucial for unraveling the stability and ecological roles of diverse ecosystems. However, the factors driving these interactions, leading to shifts in species fitness and ecological niches, remain inadequately explored. We demonstrate that metabolic similarity serves as a key driver of niche deformation between bacterial species. Resource availability emerges as a pivotal parameter, affecting interactions within the community. Our findings reveal heightened microbial inhibition and more negative interactions under resource-limited conditions. The prevalent facilitation is observed under conditions of high resource availability, underscoring the potential for niche expansion in such contexts. These findings emphasize that metabolic similarity induces varying degrees of resource competition, thereby altering pairwise interactions within the synthetic community and potentially modulating bacterial niches. Our workflow has broad implications for understanding the roles of metabolic similarity and resource availability in microbial interactions and for designing synthetic microbial communities.

Stereoselective Double Functionalization of Geminated C(sp3)‐Organodimetallic Linchpins

AbstractGeminated C(sp3)‐organodimetallics can serve as dinucleophilic linchpins for the rapid assembly of complex molecular structures through two consecutive electrophilic substitution reactions with two different electrophiles. Implementation of these double functionalization sequences in a stereoselective manner to develop tools for asymmetric synthesis has attracted considerable interest from the synthetic community over the last decade. The focus has been put mostly on 1,1‐bimetallic reagents containing boron, zinc or zirconium, and different strategies have been applied for such a purpose, including the diastereoselective transformation of enantioenriched chiral reagents or the enantioselective conversion of achiral or racemic derivatives. Asymmetric catalysis is at stake in most of the approaches developed. In this review article, we highlight the key advances in the development of 1,1‐bimetallic linchpins as tools for asymmetric synthesis, emphasizing the underlying general concepts.

Integrated application of synthetic community reduces consumption of herbicide in field Phalaris minor control

Integrated application of synthetic community reduces consumption of herbicide in field Phalaris minor control

Interplay between Amaryllidaceae alkaloids, the bacteriome and phytopathogens in Lycoris radiata.

Alkaloids are a large group of plant secondary metabolites with various structures and activities. It is important to understand their functions in the interplay between plants and the beneficial and pathogenic microbiota. Amaryllidaceae alkaloids (AAs) are unique secondary metabolites in Amaryllidaceae plants. Here, we studied the interplay between AAs and the bacteriome in Lycoris radiata, a traditional Chinese medicinal plant containing high amounts of AAs. The relationship between AAs and bacterial composition in different tissues of L. radiata was studied. In vitro experiments revealed that AAs have varying levels of antimicrobial activity against endophytic bacteria and pathogenic fungi, indicating the importance of AA synthesis in maintaining a balance between plants and beneficial/pathogenic microbiota. Using bacterial synthetic communities with different compositions, we observed a positive feedback loop between bacteria insensitive to AAs and their ability to increase accumulation of AAs in L. radiata, especially in leaves. This may allow insensitive bacteria to outcompete sensitive ones for plant resources. Moreover, the accumulation of AAs enhanced by insensitive bacteria could benefit plants when challenged with fungal pathogens. This study highlights the functions of alkaloids in plant-microbe interactions, opening new avenues for designing plant microbiomes that could contribute to sustainable agriculture.

Synthetic bacterial community derived from Astragalus mongholicus and plant-plant interactions inhibit cadmium uptake by modulating gene expression, antioxidant system and carbohydrate metabolism under cadmium contaminated soil

In this study we evaluated an alternative strategy to inhibit cadmium (Cd) uptake with synthetic bacterial community (SynCom) in cereal-legume intercropping under Cd contaminated soil. The results exhibited that intercropping coupled with SynCom inoculation promoted wheat biomass and inhibits Cd uptake in shoot (−65.05%), root (−34.66%) and grain (−74.45%) over monoculture without inoculation under Cd stress. However, antioxidant enzyme activities were significantly increased with SynCom inoculation in wheat grown on Cd contaminated soil irrespective of intercropping. SynCom inoculation considerably increased cytoplasmic invertase, vacuolar invertase, hexokinase, phosphoglucoisomerase, glucose-6-phosphate dehydrogenase, phosphofructokinase and SuSy while decreased the activities of ADP-Glucose pyrophosphorylase, aldolase, fructokinase, phosphoglucomutase and UDP-glucose pyrophorylase irrespective of intercropping under Cd stress. Furthermore, the expressions of gene encoding heavy metal stress were significantly decreased with the SynCom inoculation in roots. The expression of TaHMA3-b in root was downregulated by SynCom inoculation in wheat grown under Cd stress. The expressions of gene encoding heavy metal stress in shoot were downregulated by SynCom inoculation over other treatments. These findings not only offered useful information for future study of interaction mechanisms between intercropping and SynCom inoculation, but also demonstrated a suitable technological approach for remediation coupled with agro-production in mildly to substantially Cd polluted soil.

Phyllosphere microbial associations improve plant reproductive success.

The above-ground (phyllosphere) plant microbiome is increasingly recognized as an important component of plant health. We hypothesized that phyllosphere bacterial recruitment may be disrupted in a greenhouse setting, and that adding a bacterial amendment would therefore benefit the health and growth of host plants. Using a newly developed synthetic phyllosphere bacterial microbiome for tomato (Solanum lycopersicum), we tested this hypothesis across multiple trials by manipulating microbial inoculation of leaves and measuring subsequent plant growth and reproductive success, comparing results from plants grown in both greenhouse and field settings. We confirmed that greenhouse-grown plants have a relatively depauperate phyllosphere bacterial microbiome, which both makes them an ideal system for testing the impact of phyllosphere communities on plant health and important targets for microbial amendments as we move towards increased agricultural sustainability. We find that the addition of the synthetic microbial community early in greenhouse growth leads to an increase in fruit production in this setting, implicating the phyllosphere microbiome as a key component of plant fitness and emphasizing the role that these bacterial microbiomes likely play in the ecology and evolution of plant communities.

2‐Hydroxypyridines as N‐ and O‐Nucleophiles in Organic Synthesis

Abstract2‐Hydroxypyridines have emerged as versatile nucleophiles in organic synthesis. The N‐ and O‐functionalization of 2‐hydroxypyridines affords straightforward and practical methods for the construction of N‐substituted 2‐pyridones and O‐substituted 2‐hydroxypyridines, which are important structural motifs in numerous natural products, pharmaceuticals and biologically active compounds. Nonetheless, the competition between N‐ and O‐functionalization of 2‐hydroxypyridines presents an inevitable and formidable challenge. In the past few decades, chemoselective N‐ and/or O‐functionalization of 2‐hydroxypyridines has received extensive attention from the synthetic community, resulting in the development of elegant and effective strategies to address this chemoselectivity. This review provides a summary of recent advancements in the realm of transition‐metal and organo‐catalyzed, as well as visible‐light promoted chemoselective functionalization of 2‐hydroxypyridines, including N‐alkylation, N‐allylation, N‐arylation, N‐alkenylation, O‐alkylation, O‐allylation, O‐arylation, and O‐alkenylation.

Analysis of the endophytic microbiota of roots and culms of two commercial sugarcane cultivars inoculated with a synthetic microbial community

The adoption of bioinputs in agriculture has aroused great interest in recent years and, in this scenario, the inoculation of crops with synthetic microbial communities (SynComs) has shown to be promising. In sugarcane crop, inoculation with nitrogen-fixing bacteria (NFB) in consortium with arbuscular mycorrhizal fungi (AMF) has shown positive results on plant development and nutrition. However, considering that the microbiota plays a fundamental role in the growth and health of the host plant, especially the endophytes, which are closely associated, few studies have explored the effects of SynCom inoculation on the endophytic microbiota of sugarcane. This study aimed to evaluate the impact of SynCom inoculation on the structure of the endophytic microbiota of sugarcane. The results of the analyses revealed that the microbiota diversity remained unchanged due to the inoculation treatment, while differences in microbial communities were found between the two evaluated commercial cultivars, RB867515 and RB92579, and between the two plant organs, roots and culms, under field conditions at the end of the first crop growth cycle (~360 days). Furthermore, microbes specifically detected in roots or culms present potential valuable applications in sugarcane cultivation in the future. Altogether, our data support that the inoculated microorganisms exerted their beneficial effects during the initial stages of plant development, which opens up space for new research with SynComs in these primordial stages of cane cropping.

The Total Synthesis of Aspidofractinine and Related Alkaloids

AbstractThe fascinating structural features and potential biological activities of aspidofractinine monoterpenoid indole alkaloids grasped the attention of synthetic community since 1964. Aspidofractinine also serves as the primary structural component to over 200 monoterpenoid indole alkaloids, in which most of these alkaloids’ total synthesis has been unexplored. In light of these facts, studies on synthetic strategies towards the complex, intriguing carbon skeleton of aspidofractinine have high implications. The intensive studies on the total synthesis of aspidofractinine alkaloids have resulted in numerous elegant strategies to construct the highly substituted hexacyclic core structure containing bicyclo[2.2.2]octane motif and three all‐carbon quaternary stereogenic centers. This review discusses all reported strategies for synthesizing aspidofractinine, and aspidofractinine‐like alkaloids.

Comprehensive Study on Solomonamides: Total Synthesis, Stereochemical Revision, and SAR Studies toward Identification of Simplified Lead.

Solomonamides, a pair of macrocyclic peptide natural products originating from marine sources, have garnered significant attention within the synthetic community owing to their marked anti-inflammatory efficacy and intricate molecular architectures. In this paper, we present a very detailed investigation into solomonamides, including the challenges associated with the total synthesis, the evolution of our synthetic strategies, structural reassignment, synthesis of all possible stereoisomeric macrocycles, biological assessment, structure-activity relationship (SAR) studies, etc. Within the ambit of this total synthesis, diverse strategies for macrocyclization were rigorously explored, encompassing the Friedel-Crafts acylation, cyclization involving the aniline NH2 moiety, macrolactamization utilizing Gly-NH2, and Heck macrocyclization methodologies. In addition, an array of intriguing chemical transformations were devised, including but not limited to photo-Fries rearrangement, Wacker oxidation, ligand-free Heck macrocyclization, oxidative cleavage of indole, synthesis of contiguous stereocenters via substrate/reagent-controlled protocols, and simultaneous making and breaking of olefinic moieties. The findings of this investigation revealed a structurally simplified lead compound. Remarkably, the lead compound, while possessing structural simplification in comparison to the intricate solomonamide counterparts, demonstrates equipotent in vivo anti-inflammatory efficacy.

In-situ substitution and community dynamics modeling for enhanced safety in Chinese rice wine brewing

This research paper focuses on the application of the “Design-Build-Test-Learn” framework to design and evaluate a synthetic microbial community aimed at studying the impact of Lactic Acid Bacteria (LAB) interactions and fitness on the formation of biogenic amines (BAs) in Chinese rice wine (CRW). The study reveals a close correlation between the assembly model of LAB and the accumulation of BAs in CRW, and multiple interactions were observed between amine-producing and non-amine-producing LAB, including commensalism, amensalism, and competition. The commensalism among amine-producing LAB was found to promote BAs accumulation through metabolic cross-feeding of amino acids. Moreover, the higher-order interaction community was designed to regulate the BAs formation effectively. For instance, the interference of Lactiplantibacillus plantarum (ACBC271) resulted in the elimination of amine-producing LAB viability, resulting in a 22% decrease (not exceeding 43.54 mg/L) in the total amount of BAs. Simulation of community dynamics models further suggests that LAB with quantitative social interactions can effectively control LAB accumulation in CRW by forecasting fluctuation in BAs generation through fitness competition and metabolic interference. Overall, this study provides valuable insights into the complex interaction networks within microbial communities in traditional fermentation ecosystems. It also proposes a novel approach for quality control of nitrogen food safety factors in fermented foods.

Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning

Plant-associated microbiomes contribute to important ecosystem functions such as host resistance to biotic and abiotic stresses. The factors that determine such community outcomes are inherently difficult to identify under complex environmental conditions. In this study, we present an experimental and analytical approach to explore microbiota properties relevant for a microbiota-conferred host phenotype, here plant protection, in a reductionist system. We screened 136 randomly assembled synthetic communities (SynComs) of five bacterial strains each, followed by classification and regression analyses as well as empirical validation to test potential explanatory factors of community structure and composition, including evenness, total commensal colonization, phylogenetic diversity, and strain identity. We find strain identity to be the most important predictor of pathogen reduction, with machine learning algorithms improving performances compared to random classifications (94-100% versus 32% recall) and non-modelled predictions (0.79-1.06 versus 1.5 RMSE). Further experimental validation confirms three strains as the main drivers of pathogen reduction and two additional strains that confer protection in combination. Beyond the specific application presented in our study, we provide a framework that can be adapted to help determine features relevant for microbiota function in other biological systems.

Bacillus velezensis WB invokes soil suppression of Fusarium oxysporum f. sp. niveum by inducing particular taxa

Fusarium wilt of watermelon caused by Fusarium oxysporum f. sp. niveum (Fon) results in a substantial economic losses in agriculture. Biological control agents (BCAs) help in controlling the infection of Fon. However, it remains unclear whether the application of BCAs can invoke soil suppression by inducing specific microbial groups concerned with disease suppression to synergistically resist fungal pathogens. The objective of this project was to determine the microbial mechanisms involved in disease suppression by BCAs. Here, we conducted pot experiments to explore Fusarium wilt in watermelon and soil microbial communities in response to different treatments. We found that the application of Bacillus velezensis WB enhanced disease suppression in nonsterilized soil. We further found that disease suppression in the WF treatment was connected to influence on the resident soil microbial communities, explicitly by causing an increase in Hyphomicrobiaceae and Chitinophagaceae. Pathogen suppression by the above two families was further studied in laboratory and pot experiments. The results showed that a synthetic community consisting of specific bacterial taxa effectively decreased the incidence of Fusarium wilt. B. velezensis WB introduction impacts the resident soil microbiome and invokes soil suppression by inducing resident microbes. Our results should help in designing synthetic microbial communities to improve soil function.

Synthetic Communities Increase Microbial Diversity and Productivity of Agave tequilana Plants in the Field

Agaves are plants native to North America that sustain life in arid and semiarid ecosystems. Previous studies revealed that cultivated plants of Agave tequilana had lower microbial diversity and functionality than wild Agave species. Here, we tested if synthetic communities (syncoms), based on microbial hubs or taxa with enriched microbial functions, could increase microbial diversity, plant health, and productivity in A. tequilana. We applied 10 syncoms to the phyllospheres of 6-month-old plants of A. tequilana in the field and monitored their development for 2 years. Amplicon sequencing of 16S-rRNA-V4 and ITS2 revealed that the inoculated syncoms played a negligible or minor role in the assembly of the prokaryotic and eukaryotic phyllospheric communities associated with A. tequilana, respectively. However, syncoms based on microbial hubs, particularly those observed in the phyllosphere associated with wild A. salmiana (PFCS), promoted microbial communities with higher alpha diversity. Some of these syncom-derived phyllospheric communities consumed a greater variety of carbon sources; had more complex co-occurrence networks; and increased the content of sugars (oBrix, a measure of productivity in agaves) in the stem and changed the leaf metabolome. Our work demonstrates that the application of syncoms formulated based on predicted microbe–microbe interactions and metagenomic analyses of microbial communities in cultivated and wild plant species represents an effective tool to improve the sustainability and productivity of crops in arid ecosystems. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Control points for design of taxonomic composition in synthetic human gut communities

Microbial communities offer vast potential across numerous sectors but remain challenging to systematically control. We develop a two-stage approach to guide the taxonomic composition of synthetic microbiomes by precisely manipulating media components and initial species abundances. By combining high-throughput experiments and computational modeling, we demonstrate the ability to predict and design the diversity of a 10-member synthetic human gut community. We reveal that critical environmental factors governing monoculture growth can be leveraged to steer microbial communities to desired states. Furthermore, systematically varied initial abundances drive variation in community assembly and enable inference of pairwise inter-species interactions via a dynamic ecological model. These interactions are overall consistent with conditioned media experiments, demonstrating that specific perturbations to a high-richness community can provide rich information for building dynamic ecological models. This model is subsequently used to design low-richness communities that display low or high temporal taxonomic variability over an extended period. A record of this paper's transparent peer review process is included in the supplemental information.

Lest We Forget-The Importance of Heteroatom Interactions in Heterocyclic Conjugated Systems, from Synthetic Metals to Organic Semiconductors.

The field of synthetic metals is, and remains, highly influential for the development of organic semiconductor materials. Yet, with the passing of time and the rapid development of conjugated materials in recent years, the link between synthetic metals and organic semiconductors is at risk of being forgotten. This review reflectson one of the key concepts developed in synthetic metals - heteroatom interactions. The application of this strategy in recent organic semiconductor materials, small molecules and polymers, is highlighted, with analysis of X-ray crystal structures and comparisons with model systems used to determine the influence of these non-covalent short contacts. The case is made that the wide range of effective heteroatom interactions and the high performance that has been achieved in devices from organic solar cells to transistors is testament to the seeds sown by the synthetic metals research community.

Enhanced specificity of Bacillus metataxonomics using a tuf-targeted amplicon sequencing approach

Bacillus species are ubiquitous in nature and have tremendous application potential in agriculture, medicine, and industry. However, the individual species of this genus vary widely in both ecological niches and functional phenotypes, which, hence, requires accurate classification of these bacteria when selecting them for specific purposes. Although analysis of the 16S rRNA gene has been widely used to disseminate the taxonomy of most bacterial species, this gene fails proper classification of Bacillus species. To circumvent this restriction, we designed novel primers and optimized them to allow exact species resolution of Bacillus species in both synthetic and natural communities using high-throughput amplicon sequencing. The primers designed for the tuf gene were not only specific for the Bacillus genus but also sufficiently discriminated species both in silico and in vitro in a mixture of 11 distinct Bacillus species. Investigating the primers using a natural soil sample, 13 dominant species were detected including Bacillus badius, Bacillus velezensis, and Bacillus mycoides as primary members, neither of which could be distinguished with 16S rRNA sequencing. In conclusion, a set of high-throughput primers were developed which allows unprecedented species-level identification of Bacillus species and aids the description of the ecological distribution of Bacilli in various natural environment.