Synthetic Community Research Articles

A synthetic bacterial community engineered from Miscanthus floridulus roots enhances ammonia nitrogen removal in ionic rare earth mine tailings.

Ammonium sulfate, as the primary leaching agent, has caused significant nitrogen pollution in rare earth elements (REEs) mining areas. Phytoremediation is a promising remediation method, relying on the synergistic relationships between plants and their root-associated microbiome. Nevertheless, harnessing the microbiome to accelerate nitrogen transformation and absorption by plants is challenging. Here, we investigated the composition, activities and culturable fraction of the root bacterial microbiome of the pioneer plant Miscanthus floridulus grown in a REEs tailing soil containing a high ammonia nitrogen (AN) concentration at 344.35mgkg-1. Based on this, we constructed a simplified synthetic microbial community (SynCom) derived from the roots of M. floridulus, possessing nitrification and denitrification capabilities, to help REEs mine plants efficiently convert pollutant AN into nutrients, thereby enhancing plant growth and AN removal. This SynCom, consisting of 10 bacterial strains, included species of the genera Burkholderia (5) Paraburkholderia (1), Curtobacterium (1), Leifsonia (1) and Sinomonas (2). As a result, this SynCom alone achieved a significant reduction of 24.8% in AN content in tailing soil. When the SynCom inoculated with plants, the reduction in AN was even more significant (32.6%), surpassing the reduction achieved solely by plants (25.5%). Moreover, live SynCom inoculation significantly increased shoot and root biomass by 39.8% and 49.7%, respectively, compared to dead SynCom inoculation. These results indicate that the reduction in AN can be attributed to the SynCom's nitrification and denitrification capabilities, as well as its ability to enhance plant nitrogen absorption by stimulating their growth. Notably, seven nitrifying and denitrifying strains of the SynCom are particularly enriched, suggesting that plant roots selectively recruit nitrogen cycle-related bacteria to accelerate nitrogen transformation and absorption. These results provide a practical solution for harnessing the synergistic relationships between plants and their root microbiome in environmental remediation efforts.

Community standards and future opportunities for synthetic communities in plant-microbiota research.

Harnessing beneficial microorganisms is seen as a promising approach to enhance sustainable agriculture production. Synthetic communities (SynComs) are increasingly being used to study relevant microbial activities and interactions with the plant host. Yet, the lack of community standards limits the efficiency and progress in this important area of research. To address this gap, we recommend three actions: (1) defining reference SynComs; (2) establishing community standards, protocols and benchmark data for constructing and using SynComs; and (3) creating an infrastructure for sharing strains and data. We also outline opportunities to develop SynCom research through technical advances, linking to field studies, and filling taxonomic blind spots to move towards fully representative SynComs.

A cross-systems primer for synthetic microbial communities.

The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current best practices in developing, implementing and evaluating SynComs across different systems, including a focus on important ethical considerations for SynCom research.

Mice colonized with the defined microbial community OMM19.1 are susceptible to Clostridioides difficile infection without prior antibiotic treatment.

Diverse gut microorganisms present in humans and mice are essential for the prevention of microbial pathogen colonization. However, antibiotic-induced dysbiosis of the gut microbiome reduces microbial diversity and allows Clostridioides difficile (C. difficile) to colonize the intestine. The Oligo-Mouse-Microbiota 19.1 (OMM19.1) is a synthetic community that consists of bacteria that are taxonomically and functionally designed to mimic the specific pathogen-free mouse gut microbiota. Here, we examined the susceptibility of OMM19.1 colonized mice to C. difficile infection (CDI) at a range of infectious doses (103, 105, and 107 spores) without prior antibiotic treatment. We found that mice colonized with OMM19.1 were susceptible to CDI regardless of the dose. The clinical scores increased with increasing C. difficile dosage. Infection with C. difficile was correlated with a significant increase in Ligilactobacillus murinus and Escherichia coli, while the relative abundance of Bacteroides caecimuris, Akkermansia muciniphila, Extibacter muris, and Turicimonas muris was significantly decreased following CDI. Our results demonstrate that the OMM19.1 community requires additional bacteria to enable C. difficile colonization resistance.IMPORTANCEThe human gut microbiota consists of a wide range of microorganisms whose composition and function vary according to their location and have a significant impact on health and disease. The ability to generate and test the defined microbiota within gnotobiotic animal models is essential for determining the mechanisms responsible for colonization resistance. The exact mechanism(s) by which healthy microbiota prevents Clostridioides difficile infection is unknown, although competition for nutrients, active antagonism, production of inhibitory metabolites (such as secondary bile acids), and microbial manipulation of the immune system are all thought to play a role. Here, we colonized germ-free C57BL/6 mice with a synthetic bacterial community (OMM19.1) that mimics the specific pathogen-free mouse microbiota. Following breeding, to enable immune system development, F1 mice were infected with three different doses of C. difficile. Our research suggests that there are additional essential microbial functions that are absent from the current OMM19.1 model.

A Review on Plant-microbe Interactions and its Defence Mechanism

Plant-microbe interactions are fundamental to plant health, growth, and defense, influencing agricultural productivity and ecosystem dynamics. These interactions range from symbiotic relationships, such as those with mycorrhizal fungi and nitrogen-fixing bacteria, to pathogenic encounters that trigger complex plant immune responses. Beneficial microbes, including rhizobacteria, mycorrhizae, and endophytes, play a crucial role in enhancing plant defenses through mechanisms like induced systemic resistance (ISR) and production of antimicrobial compounds. Advances in our understanding of these interactions have enabled the development of innovative strategies for crop protection, such as the use of biocontrol agents and microbial inoculants. Additionally, plant breeding and genetic engineering have been employed to introduce resistance genes and modify plant immune responses, resulting in disease-resistant varieties. However, harnessing plant-microbe interactions for sustainable agriculture faces challenges due to the complexity of these interactions in natural environments and the influence of abiotic factors. Limitations in research methodologies, such as difficulties in isolating and studying unculturable microbes, further complicate the translation of findings into practical applications. To overcome these barriers, future research should focus on integrating multi-omics approaches, employing synthetic microbial communities (SynComs), and leveraging CRISPR/Cas technologies for precise manipulation of plant and microbial genes. Microbiome engineering holds promise for promoting beneficial microbial communities, improving plant resilience, and reducing chemical inputs in agriculture. Addressing these challenges will be critical for realizing the full potential of plant-microbe interactions, ultimately contributing to sustainable crop production, improved food security, and ecosystem health. This review highlights current advances, applications, and future directions in the study of plant-microbe interactions, emphasizing their significance for modern agriculture.

Mixed and membrane-separated culturing of synthetic cyanobacteria-yeast consortia reveals metabolic cross-talk mimicking natural cyanolichens

Metabolite exchange mediates crucial interactions in microbial communities, significantly impacting global carbon and nitrogen cycling. Understanding these chemically-mediated interactions is essential for elucidating natural community functions and developing engineered synthetic communities. This study investigated membrane-separated bioreactors (mBRs) as a novel tool to identify transient metabolites and their producers/consumers in mixed microbial communities. We compared three co-culture methods (direct mixed, 2-chamber mBR, and 3-chamber mBR) to grow a synthetic binary community of the cyanobacterium Synechococcus elongatus PCC 7942 and the fungus Rhodotorula toruloides NBRC 0880, as well as axenic S. elongatus. Despite not being natural lichen constituents, these organisms exhibited interactions resembling those in cyanolichens. S. elongatus fixed CO2 into sugars as the primary shared metabolite, while R. toruloides secreted various biochemicals, predominantly sugar alcohols, mirroring the metabolite exchange observed in natural lichens. The mBR systems successfully captured metabolite gradients and revealed rapidly consumed compounds, including TCA cycle intermediates and amino acids. Our approach demonstrated that the 2-chamber mBR optimally balanced metabolite exchange and growth dynamics. This study provides insights into cross-species metabolic interactions and presents a valuable tool for investigating and engineering synthetic microbial communities with potential applications in biotechnology and environmental science.

Resource sharing of an infant gut microbiota synthetic community in combinations of human milk oligosaccharides.

Quickly after birth, the gut microbiota is shaped via species acquisition and resource pressure. Breastmilk, and more specifically, human milk oligosaccharides are a determining factor in the formation of microbial communities and the interactions between bacteria. Prominent human milk oligosaccharide degraders have been rigorously characterized, but it is not known how the gut microbiota is shaped as a complex community. Here, we designed BIG-Syc, a synthetic community of 13 strains from the gut of vaginally born, breastfed infants. BIG-Syc replicated key compositional, metabolic, and proteomic characteristics of the gut microbiota of infants. Upon fermentation of a 4 and 5 human milk oligosaccharide mix, BIG-Syc demonstrated different compositional and proteomic profiles, with Bifidobacterium infantis and Bifidobacterium bifidum suppressing one another. The mix of 5 human milk oligosaccharides resulted in a more diverse composition with dominance of B. bifidum, whereas that with 4 human milk oligosaccharides supported the dominance of B. infantis, in 4 of 6 replicates. Reintroduction of bifidobacteria to BIG-Syc led to their engraftment and establishment of their niche. Based on proteomics and genome-scale metabolic models, we reconstructed the carbon source utilization and metabolite and gas production per strain. BIG-Syc demonstrated teamwork as cross-feeders utilized simpler carbohydrates, organic acids, and gases released from human milk oligosaccharide degraders. Collectively, our results showed that human milk oligosaccharides prompt resource-sharing for their complete degradation while leading to a different compositional and functional profile in the community. At the same time, BIG-Syc proved to be an accurate model for the representation of intra-microbe interactions.

Metagenomic discovery of microbial eukaryotes in stool microbiomes.

Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.

Mitigation of microplastic toxicity in soybean by synthetic bacterial community and arbuscular mycorrhizal fungi interaction: Altering carbohydrate metabolism, hormonal transduction, and genes associated with lipid and protein metabolism

Microplastics (MPs) have become ubiquitous environmental pollutants, eliciting concerns about their negative impacts on terrestrial and agroecosystems. However, employing sustainable remediation approaches holds the potential to mitigate these negative impacts and bolster MPs tolerance in both the seeds and vegetative structures of plants. The current investigation explores the impact of arbuscular mycorrhizal fungi (AMF) and synthetic bacterial community (SynCom) as potential alleviators of MP-induced stress. Results exhibited that co-applied SynCom and AMF, resulted in the highest plant biomass, leaf area, pod per plant, and 100-seed weight under control (no MPs) and MPs stress. The combined application of SynCom and AMF enhanced colonization, association, and arbuscule abundance in the non-stressed plants (no MPs) as compared to stressed plants. The sole or co-application of SynCom and AMF enhanced the primary metabolites content and mitigated the MPs-induced reduction in soluble sugars, lipids, protein, and oil contents. Soybean inoculation stimulated the genes expression involved in lipid and protein biosynthesis, while a contradictory drift was noted for genes associated with lipid and protein degradation, underpinning the observed increment in protein and lipid content. Soybean inoculated with AMF exhibited the utmost α-amylase and β-amylase activities, demonstrating enhanced osmolyte (soluble sugar) production, mainly under MPs stress. Remarkably, sole or co-application further reinforces the positive effect of MPs stress on the osmoprotectants and antioxidant levels, for instance, phenol, flavonoid, glycine betaine contents, and glutathione-S-transferase (GST) activities. Subsequent to the stress release, a stress hormones known as abscisic acid (ABA) reduced in the seeds of inoculated soybean while gibberellin (GA), trans-zeatin riboside (ZR), and indole acetic acid (IAA) were increased. Therefore, it is concluded that the combined application of SynCom and AMF protected the soybean plants from MPs-induced oxidative damage by upregulating osmoprotectants and antioxidant levels. This study provides insights into the potential of sustainable remediation approaches in alleviating the complex impact of MPs on soybean, contributing to future strategies for environmental sustainability. Future studies could explore the optimization of SynCom and AMF formulations for different crops and environmental conditions, potentially leading to practical applications in sustainable agriculture and pollution management.

Microbial diversification is maintained in an experimentally evolved synthetic community.

In nature, bacteria live in microbial communities and interact with other species, for example, through the exchange of resources leaked into the external environment (i.e., cross-feeding interactions). The role that these cross-feeding interactions play in shaping patterns of diversification remains understudied. Using a simple bacterial system in which one species cross-feeds resources to a second species (commensal species), we showed that the commensal species diversified into two subpopulations that persisted only when the cross-feeder partner was present. We further observed loss-of-function mutations in flagellar genes that were fixed in monocultures but not in co-cultures. Our findings suggest that cross-feeding species influence patterns of diversification of other species. Given that nutrient leakage is pervasive in microbial communities, the findings from this study have the potential to extend beyond our specific bacterial system. Importantly, our study has contributed to answering the larger question of whether species evolved differently in isolation versus when interacting with other species.

Mucin-driven ecological interactions in an in vitro synthetic community of human gut microbes.

Specific human gut microbes inhabit the outer mucus layer of the gastrointestinal tract. Certain residents of this niche can degrade the large and complex mucin glycoproteins that constitute this layer and utilise the degradation products for their metabolism. In turn, this microbial mucin degradation drives specific microbiological ecological interactions in the human gut mucus layer. However, the exact nature of these interactions remains unknown. In this study, we designed and studied an in vitro mucin-degrading synthetic community that included mucin O-glycan degraders and cross-feeding microorganisms by monitoring community composition and dynamics through a combination of 16S rRNA gene amplicon sequencing and qPCR, mucin glycan degradation with PGC-LC-MS/MS, production of mucin-degrading enzymes and other proteins through metaproteomics, and metabolite production with HPLC. We demonstrated that specialist and generalist mucin O-glycan degraders stably co-exist and found evidence for cross-feeding relationships. Cross-feeding on the products of mucin degradation by other gut microbes resulted in butyrate production, hydrogenotrophic acetogenesis, sulfate reduction and methanogenesis. Metaproteomics analysis revealed that mucin glycan degraders Akkermansia muciniphila, Bacteroides spp. and Ruminococcus torques together contributed 92% of the total mucin O-glycan degrading enzyme pool of this community. Furthermore, comparative proteomics showed that in response to cultivation in a community compared to monoculture, mucin glycan degraders increased carbohydrate-active enzymes whereas we also found indications for niche differentiation. These results confirm the complexity of mucin-driven microbiological ecological interactions and the intricate role of carbohydrate-active enzymes in the human gut mucus layer.

Synergy between Arbuscular Mycorrhizal Fungi and Rhizosphere Bacterial Communities Increases the Utilization of Insoluble Phosphorus and Potassium in the Soil by Maize.

Arbuscular mycorrhizal (AM) fungi can enhance plant uptake of phosphorus (P) and potassium (K), but it is not yet clear whether rhizosphere bacteria can enhance the ability of AM fungi to acquire insoluble P and K from the soil. Here, pot experiments confirmed that AM fungus-promoted insoluble P and K uptake by plants requires rhizosphere bacteria. The changes of rhizosphere bacterial communities associated with AM fungi were explored by 16S rRNA amplicon sequencing and metagenomic sequencing. Five core bacteria genera identified were involved in P and K cycles. Synthetic community (SynCom) inoculation revealed that SynCom increased soil available P and K and its coinoculation with AM fungi increased P and K concentration in the plants. This study revealed that AM fungi interact with rhizosphere bacteria and promote insoluble P and K acquisition, which provided a foundation for the application of AM fungal-bacterial biofertilizers and was beneficial for the sustainable development of agriculture.

Simulation of Epidemic Dynamics Using a Multi-Agent Model: Analysis of Social Distancing Strategies and Their Impacts on Public Health and Economy

Infectious disease epidemics have played a crucial role in shaping public health responses, particularly in global health crises. This study emerges as part of the efforts to prepare effective responses to potential future pandemics, leveraging lessons learned during the COVID-19 crisis. The research uses an adapted compartmental epidemiological model and a synthetic multi-agent community to investigate how social variables influence epidemic forecasts in socioeconomically vulnerable regions. Focusing on the simulation of epidemic dynamics in the socio-economically disadvantaged neighbourhood of Ilha Joana Bezerra in Recife, this study examines the impacts of social distancing strategies and other control measures, such as face masks and moderate social isolation. Through the adapted SEPAI3R3O model, which includes compartments for pre-symptomatic and asymptomatic states, this study provides a detailed analysis of disease dynamics in contexts characterised by high social vulnerability. The results underscore the importance of public health policies adapted to socio-economic factors, emphasising the need for continuous preparedness to manage future epidemic threats in vulnerable communities effectively.

A Comprehensive Review of Synthetic Approaches Toward Lamellarin D and its Analogous

AbstractLamellarin D, a naturally occurring molecule, isolated from marine molluscs, it exhibits potent pharmacological activities, such as topoisomerase I inhibition, antiproliferation, antiviral, insecticidal, antimetastatic and anticancer effects, making it a promising candidate for drug development. This review explores the synthesis of Lamellarin D employing various methodologies. These synthetic approaches have enabled researchers to access Lamellarin D and its analogous efficiently, facilitating further investigation into their biological properties. Our study summarizes the major contributions of these efforts to the larger synthetic community, primarily focusing on general synthetic techniques toward the Lamellarin D and its counterpart since its isolation in 1997 to the present.

Lycium barbarum arabinogalactan inhibits Escherichia coli and improves Lactobacillus plantarum growth in a defined microbial model of human gut microbiome

Arabinogalactan from Lycium barbarum (LBP-3) is the major biological activity component and contributes to maintaining intestinal immune homeostasis by targeting gut microbiota and their metabolites. However, it is still a big challenge to know the specific ecological microbe-metabolite interaction regulated by LBP-3 due to the host complex diet webs and lots of unidentified intestinal bacteria. Therefore, the present study constructed a defined microbial consortium, composing of symbiotic Bacteroides caccae, Phocaeicola vulgatus, B. thetaiotaomicron, B. uniformis, B. ovatus, Lactobacillus plantarum and Escherichia coli in vitro, to investigate the impact of LBP-3 on the interactions of species and their metabolites. The utilization of LBP-3 by the defined microbial consortium of 7 intestinal species was 22.5%. Full-length 16S rRNA analysis demonstrated that LBP-3 significantly modulated the composition of synthetic bacterial community, especially inhibiting the level of opportunistic pathogenic E. coli and improving the relative abundance of probiotic L. plantarum and all Bacteroidetes species except B. ovatus. LBP-3 remarkedly influenced 27 differential metabolites, mainly belong to amino acids, peptides and analogues (37.04%) and carboxylic acid and derivatives (7.41%). Moreover, targeted metabolomics revealed that the levels of acetate, propionate, tryptophan and 5-methylthioadenosine were improved by LBP-3. In addition, LBP-3 modulated the pathways of tryptophan metabolism, cysteine and methionine metabolism, and biosynthesis of siderophore group nonribosomal peptides. Notably, some amino acids (e.g., proline and glutamate) and their related metabolic pathways (e.g., arginine and proline metabolism) altered by LBP-3 were significantly correlated with the levels of species, such as B. uniformis, P. vulgatus, and B. thetaiotaomicron.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.

The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (~1:100), but a much larger ratio of phage genomes to bacterial genomes (~4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage, phage-plasmids, etc.). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occurs at a low average rate (~0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone, while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.

Elucidating core microbiota in yellow wine (Huangjiu) through flavor-oriented synthesis and construction of microbial communities

Huangjiu, a traditional Chinese alcoholic beverage with a history spanning thousands of years, holds significant cultural and economic value in China. Despite its importance, the complexity of Huangjiu fermentation and the intricate interactions within its microbial community remain underexplored. This study addresses this gap by identifying the core volatile organic compounds (VOCs) and key microorganisms that define the flavor profile of Huangjiu. We employed HS-SPME-GC–MS along with aroma reconstitution and omission experiments to identify core VOCs, including Isobutanol, Isoamyl alcohol, β-Phenylethanol, and others. Metagenomic sequencing combined with QPCR was used to analyze microbial communities, revealing the temporal and spatial dynamics during fermentation. A synthetic microbial community model was constructed using the core microbes identified: Saccharomyces cerevisiae, Lactobacillus brevis, Saccharopolyspora rectivirgula, Bacillus subtilis, Leuconostoc citreum, Lactobacillus plantarum, Lactobacillus curvatus, Lactobacillus casei, and Aspergillus oryzae. This model successfully replicated Huangjiu’s core VOCs and sensory characteristics, increased alcohol content, and reduced acidity. Our study contributes valuable insights into the microbial influences on Huangjiu quality, paving the way for its enhanced production and providing a foundation for future research in fermented beverages.

The Role of Phosphate-Solubilizing Microbial Interactions in Phosphorus Activation and Utilization in Plant-Soil Systems: A Review.

To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant-soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. The application of phosphate-solubilizing microorganisms (PSMs) is emphasized for their role in phosphorus activation and plant growth promotion. A focus is placed on microbial interactions as an entry point to regulate the functional rhizosphere microbiome, introducing the concept of synthetic communities. This approach aims to deepen the understanding of PSM interactions across plant root, soil, and microbial interfaces, providing a theoretical foundation for the development and application of biological regulation technologies to enhance phosphorus utilization efficiency.

Paenibacillus polymyxa J2-4 induces cucumber to enrich rhizospheric Pseudomonas and contributes to Meloidogyne incognita management under field conditions.

Root knot nematodes (RKNs) pose a great threat to agricultural production worldwide. The bacterial nematocides have received increasing attention due to their safe and efficient control against RKNs. Here, we investigated the biocontrol efficacy of Paenibacillus polymyxa J2-4 against Meloidogyne incognita in the field and analyzed the rhizosphere microbiome of cucumber under nematode infection after application of the J2-4 strain. Furthermore, a biomarker strain of Pseudomonas spp. was isolated from the J2-4-inoculated rhizosphere soil, and its nematocidal activity and growth-promoting effect on host plants were determined. In addition, chemotaxis assay of P. fluroescens ZJ5 toward root exudates was carried out. The field experiment demonstrated that P. polymyxa J2-4 could effectively suppressed gall formation in cucumber plants, with the galling index reduced by 67.63% in 2022 and 65.50% in 2023, respectively, compared with controls. Meanwhile, plant height and yield were significantly increased in J2-4 treated plants compared with controls. Metagenomic analysis indicated that J2-4 altered the rhizosphere microbial communities. The relative abundance of Pseudomonas spp. was notably enhanced in the J2-4 group, which was consistent with Linear discriminant analysis Effect Size results that Pseudomonas was determined as one of the biomarkers in the J2-4 group. Furthermore, the ZJ5 strain, one of the biomarker Pseudomonas strains, was isolated from the J2-4-inoculated rhizosphere soil and was identified as Pseudomonas fluorescens. In addition, P. fluorescens ZJ5 exhibited high nematicidal activity in vitro and in vivo, with 99.20% of the mortality rate of M. incognita at 24 h and 69.75% of gall index reduction. The biocontrol efficiency of the synthetic community of ZJ5 plus J2-4 was superior to that of any other single bacteria against M. incognita. Additionally, ZJ5 exhibited great chemotaxis ability toward root exudates inoculated with J2-4. Paenibacillus polymyxa J2-4 has good potential in the biological control against M. incognita under field conditions. Enrichment of the beneficial bacteria Pseudomonas fluorescens ZJ5 in the J2-4-inoculated rhizosphere soil contributes to M. incognita management. © 2024 Society of Chemical Industry.

Concise and Modular Chemoenzymatic Total Synthesis of Bisbenzylisoquinoline Alkaloids.

The bisbenzylisoquinoline alkaloids (bisBIAs) have attracted tremendous attention from the synthetic community due to their diverse and intriguing biological activities. Herein, we report the convergent and modular chemoenzymatic syntheses of eight bisBIAs bearing various substitutes and linkages in 5-7 steps. The gram-scale synthesis of various well-designed enantiopure benzylisoquinoline monomers was accomplished through an enzymatic stereoselective Pictet-Spengler reaction, followed by regioselective enzymatic methylation or chemical functionalization in a sequential one-pot process. A modified intermolecular copper-mediated Ullmann coupling enabled the concise and efficient total synthesis of five different linear bisBIAs with either head-to-tail or tail-to-tail linkage. A biomimetic oxidative phenol dimerization selectively formed the sterically hindered, electron-rich diaryl ether bond, and subsequent intramolecular Suzuki-Miyaura domino reaction or Ullmann coupling facilitated the first enantioselective total synthesis of three macrocyclic bisBIAs, including ent-isogranjine, tetrandrine and O-methylrepandine. This study highlights the great potential of chemoenzymatic strategies in the total synthesis of diverse bisBIAs and paves the way to further explore the biological functions of these natural products.