Microbial Genes Research Articles

Genes involved in carbon, nitrogen, and sulfur cycling in an important estuarine ecosystem show coherent shifts in response to changes in environmental conditions

AbstractWhile metagenomics can provide insight into microbial community metabolic potential, understanding factors that influence gene abundance is necessary to maximize the information gained from this analysis. Gene abundances are influenced by chemical or physical conditions along with other factors, such as copy number variation between taxa, methodological biases, or issues associated with identification and classification. Here, we identify major drivers of spatiotemporal shifts in microbial gene relative abundance from multiple months, sites, and depths within Chesapeake Bay in 2017 using shotgun metagenomics. We compared changes in relative abundance of key genes for bacterial photosynthesis, nitrogen, and sulfur metabolism with each other and measured environmental variables. Major drivers of differences in key metabolic gene abundances are associated with environmental variables that largely change with depth and season (e.g., temperature, oxygen, phosphate). For sulfur oxidation, bacterial photosynthesis, and denitrification, genes within each process are generally significantly correlated with each other and with several environmental variables. For other processes, such as nitrification, nitrogen fixation, and dissimilatory nitrate reduction to ammonium, genes that encode enzymes within the same pathway are not well correlated. The lack of correlation typically results from differences in identified taxa carrying these genes, suggesting modular pathway structure, methodological errors, or discrepancies in gene copy number between taxonomic groups. To be suitable indicators of biogeochemical processes for models, genes or pathways should be strongly correlated with environmental variables and specific to and inclusive of all taxa mediating the associated process.

Impact of continuous cropping on tobacco growth, stress resistance, and soil microecological structure

Tobacco fields have been continuously cropped for several years because of the high demand for tobacco leaves and limited land resources. To explore the effects of continuous cropping on tobacco growth and soil microecological community structure, this study compared the agronomic traits and physiological resistance characteristics of tobacco plants grown in noncontinuous cropping soil and soil with different continuous cropping years. High-throughput sequencing technology was used to analyze and predict the microbial community structure and functional gene variation patterns of tobacco soil. The results demonstrated that continuous cropping significantly impacted the average height, leaf area, and stem diameter of tobacco plants, as well as the contents of malondialdehyde, hydrogen peroxide, and glutathione in tobacco leaves that were continuously cropped. The relative abundances of Proteobacteria, Bacteroidetes, and Gemmatimonadetes in tobacco soil decreased with an increase in continuous cropping years, while relative abundance of Acidobacteria increased. The biodiversity index of tobacco soil samples showed a decreasing trend with an increase in continuous cropping years, with the sample with the longest continuous cropping year (33 years) having the lowest biodiversity index. Prediction of the potential functions of soil samples with different continuous cropping years revealed that the Z-scores of each pathway in noncontinuous cropping soil samples ranged from 1.12 to 0.078, while those in 33-year continuous cropping samples decreased from −0.10 to −1.41. Our findings indicate that continuous cropping has negative impacts on soil health and microecology, leading to a reduction in beneficial microbial population and microbial diversity.

The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs

Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc × (Landrace × Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including AIF1L, ASS1, and QRFP were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between CCAR2, EGR3, GSTM3, and GPR61 genes and the abundance of microorganisms, such as Trueperella, Victivallis, and Erysipelatoclostridium. In addition, six microbial genera linked to growth and feed efficiency were identified as follows Lachnospiraceae_UCG-005, Prevotellaceae_UCG-003, Prevotellaceae_NK3B31_group, Prevotella_1, Prevotella_9, and Veillonella. Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding.

Enhancing the use of phosphate rock through microbially-mediated compost transformation to improve agronomic and economic profitability in Sub-Saharan Africa

Soil degradation and limited access to chemical fertilizers partly explain the persistently low crop yields in Sub-Saharan Africa. To provide local farmers with alternative fertilizer options, this study examined the impact of locally sourced fertilizers on sorghum productivity and soil health. Treatments were set up in a completely randomized block design with five replications each. These treatments included Burkina phosphate rock (BPR), calcined BPR (Cal-BPR), triple super phosphate (TSP), four types of phosphocomposts, and an unfertilized phosphate control (Control). The phospho-composts, prepared during 4 months in advance, were as follows: Comp-1 (sorghum straw + BPR + sorghum rhizosphere soil and roots), Comp-2 (sorghum straw + Cal-BPR + sorghum rhizosphere soil and roots), Comp-3 (sorghum straw + BPR + chicken manure), and Comp-4 (sorghum straw + Cal-BPR + chicken manure). They were applied at a rate of 2.5 t ha−1 at sowing, alongside BPR, Cal-BPR, and TSP that provided 23 kg P2O5 ha−1. Urea and potassium chloride were added 15 days after sowing (DAS) to all treatments to standardize nitrogen and potassium levels to 37 kg N ha−1 and 14 kg K2O ha−1. Soil properties were evaluated using the samples collected at 42, 70, and 120 DAS. Rhizosphere soil showed higher bacterial and fungal abundance than bulk soil, particularly in compost treatments. Comp-4 notably improved soil properties, including increased phosphorus-cycling microbial genes, available phosphorus, cation exchange capacity, and pH, and it produced the highest sorghum grain yield. However, Comp-3 offered superior economic benefits, with higher net returns from grain sales. Overall, phosphocomposts improve soil health and boost sorghum yield in Sub-Saharan Africa. Calcined BPR-chicken manure-enriched compost may be used to increase crop yields. However, the study shows that BPR-chicken manure-enriched compost provides a more cost-effective solution for soil revitalization and sustainable food production in infertile soils in the region.

Dose-dependent effect of spent coffee grounds on intake, apparent digestibility, fermentation pattern, methane emissions, microbial protein supply and antioxidant status in Latxa sheep.

Spent coffee grounds (SCG), a by-product rich in polyphenols, can form part of enteric CH4 mitigation strategies while promoting the circular economy. This study aimed to evaluate the effect of 3 levels of SCG inclusion in the concentrate on enteric CH4 production, feed intake, apparent digestibility, ruminal fermentation pattern, microbial protein supply and gene expression of immune and antioxidant markers in peripheral blood of dry dairy ewes. In a replicated 4 × 4 Latin square design, 8 non-productive Latxa ewes were assigned to a concentrate that differed in the level of SCG: Control (0g/kg DM), SCG100 (100g/kg DM), SCG150 (150g/kg DM) and SCG200 (200g/kg DM). In each period, 14 days of adaptation were allowed, followed by 7 days in individual metabolic cages, and 3 days in respiratory chambers. To avoid a carry-over effect a minimum of 7 days were allotted between periods in which ewes consumed control concentrate and grass hay. Total organic matter intake (OMI) and CH4 emissions (g/d) presented a quadratic response (P=0.008 and P<0.001, respectively) to increasing levels of SCG in the feed. However, when CH4 emissions were corrected for OMI, a linear decrease was observed with increasing levels of SCG in the concentrate (P=0.009). This reduction in CH4 emissions (g/kg OMI) could be explained by the linear decrease (P=0.034) observed in apparent digestibility of organic matter (OM), particularly in crude protein (CP) and starch (P=0.002 and P=0.003, respectively), with increasing levels of SCG in the concentrate. No significant response was found on CH4 emissions corrected for digestible OM and on ruminal fermentation pattern. Regarding microbial protein supply, a linear increase in microbial protein supply efficiency (P=0.008) was observed with increasing levels of SCG in the concentrate. Moreover, SCG inclusion linearly reduced interleukin 10 (P=0.031), nuclear factor E2-related factor 2 (P=0.007), nuclear factor kappa β (P=0.014), superoxide dismutase 1 (P=0.015) gene expression and tended to linearly reduce those of tumor necrosis factor-α (P=0.074) and glutathione peroxidase 1 (P=0.082). In conclusion, inclusion of SCG up to 200g/kg in the concentrate did not modify ruminal fermentation pattern, but linearly reduced CH4 emissions per kg of OMI, due to a linear decrease in apparent digestibility of CP and starch. Moreover, linearly increased the efficiency of microbial supply and improved sheep's blood antioxidant-immune status.

Nitrogen Addition Increased the Greenhouse Gas Emissions of Permafrost Peatland Due to the Abundance of Soil Microbial Functional Genes Increasing in the Great Khingan Mountains, Northeast China

Permafrost peatlands are sensitive to changes in nitrogen levels because they are largely nitrogen-limited ecosystems. However, the microbial mechanisms by which the addition of nitrogen increases the emission of greenhouse gasses from permafrost peatlands remain unclear. This study was conducted to decipher the relationship between greenhouse gas emissions and soil microorganisms under nitrogen addition. Here, we performed a 154-day experimental investigation in order to assess the release of greenhouse gasses such as CO2, CH4, and N2O from the soils. Additionally, we examined the correlation between the rates of these gas emissions and the presence of crucial microbial functional genes in the soil. The results showed that the addition of low (0.01 g kg−1), medium (0.02 g kg−1), and high (0.04 g kg−1) levels of nitrogen increased the cumulative CO2 emissions by 2.35%–90.42%, respectively. The cumulative emissions of CH4 increased by 17.29%, 25.55% and 21.77%, respectively. The cumulative emissions of N2O increased 2.97, 7.49 and 7.72-fold. The addition of nitrogen increased the abundance of functional genes in the bacteria, fungi, methanogens, denitrifying bacteria, and nitrogen-fixing bacteria in soil by modifying abiotic soil variables and providing sufficient substrates for microorganisms. The results indicated that the addition of nitrogen can significantly promote the emission of greenhouse gasses by increasing the abundance of functional microbial genes in the soil of permafrost peatlands. These findings highlight the importance of considering nitrogen deposition and the nitrogen released from thawing permafrost when predicting the future greenhouse gasses emitted from permafrost peatlands.

Analyses of the gut microbial composition of domestic pig louse Haematopinus suis

Haematopinus suis is an obligatory ectoparasite of the domestic pig, serving as a vector of several swine pathogens and posing great threats to the pig industry. The gut microbiome of lice is thought of an important mediator of their healthy physiology. However, there is a great paucity of lice-associated microbial communities’ structure and function. The current study aimed to profile the gut microbiome and to understand the microbial functions of swine lice by metagenomic sequencing and bioinformatics analyses. In total, 102,358 (77.2 %) nonredundant genes were cataloged, by contrast, only a small proportion of genes were assigned to microbial taxa and functional assemblages. Bacteria of known or potential public health significance such as Anaplasma phagocytophilum, Chlamydia trachomatis, Waddlia chondrophila, Bacillus cereus, and Leptotrichia goodfellowii were observed in all samples. The integrated microbial profile further illustrated the evolutionary relevance of endosymbionts and detailed the functional composition, and findings suggested H. suis may acquire adenosylcobalamin by feeding due to an adenosylcobalamin synthesis defect and a lack of complete synthases of endosymbionts. Sucking lice contained fewer functional genes compared with ticks and fleas probably because of the obligate host specificity of parasitic lice. In addition, the genes from the intestines contained encompassed most of the microbial functional genes in sucking lice. A wide range of unknown taxonomic and functional assemblages were discovered, which improves our understanding related to microbial features and physiological activities of sucking lice. In general, this study increases the characterization of the microbiota of lice and offers clues for preventing and controlling lice infestation in swine production in the future.

Re-aerobic treatment and dissolved oxygen regulation in full-scale aerobic-hydrolysis and denitrification-aerobic process for achieving simultaneous detoxification and nitrification of coking wastewater

The biological treatment of coking wastewater is a challenge. The application of prepositioned aerobic process has rarely been systematically reported, among which the detoxification and nitrification performance of the prepositioned aerobic unit (O1) is worthy of investigation. Results indicate that O1 achieves stable simultaneous detoxification and nitrification by regulating the dissolved oxygen, effectively maintaining ammonification, nitrosation, and complete nitrification phases. Microbial community structure, metabolic pathways and functional genes showed different preferences at different phases. High dissolved oxygen concentrations (2.20–3.00 mg/L) benefited the enrichment of carbon and nitrogen related major metabolic pathways and functional genes. BOD5/CODCr ratio, dissolved oxygen and toxic pollutants together shaped microbial community structure and nitrogen transformation processes. Based on the principle of DO regulation, it could assemble a biotransformation compartment for nitrogen removal from complex wastewaters through a pollutant detoxification mechanism of rapid microbial proliferation，and provides a promising approach for toxic industrial wastewater.

Flue-cured tobacco intercropping with insectary floral plants improves rhizosphere soil microbial communities and chemical properties of flue-cured tobacco

BackgroundContinuous cropping of the same crop leads to land degradation. This is also called the continuous-cropping obstacle. Currently, intercropping tobacco with other crops can serve as an effective strategy to alleviate continuous cropping obstacles.ResultsIn this study, tobacco K326 and insectary floral plants were used as materials, and seven treatments of tobacco monoculture (CK), tobacco intercropped with Tagetes erecta, Vicia villosa, Fagopyrum esculentum, Lobularia maritima, Trifolium repens, and Argyranthemum frutescens respectively, were set up to study their effects on rhizosphere soil chemical properties and composition and structure of rhizosphere soil microbial community of tobacco. The 16 S rRNA gene and ITS amplicons were sequenced using Illumina high-throughput sequencing. tobacco/insectary floral plants intercropping can influence rhizosphere soil chemical properties, which also change rhizosphere microbial communities. The CK and treatment groups tobacco rhizosphere soil microorganisms had significantly different genera, such as tobacco intercropping with T. repens and A. frutescens significantly increased the number of Fusarium and intercropping T. erecta, V. villosa, L. maritima, T. repens, and A. frutescens significantly increased the number of Sphingomonas and unknown Gemmatimonadaceae. Additionally, intercropping T. erecta, V. villosa and L. maritima changed the rhizosphere fungal and bacteria community and composition of tobacco and the positive correlation between tobacco rhizosphere the genera of fungi and bacterial were greater than CK. The pathway of the carbohydrate metabolism, amino acid metabolism, and energy metabolism in rhizosphere bacteria were significantly decreased after continuous cropping. Fungal symbiotic trophic and saprophytic trophic were significantly increased after intercropping V. villosa, L. maritima and plant pathogen and animal pathogen were increased after intercropping T. repens and A. frutescens. Additionally, bacterial and fungal communities significantly correlated with soil chemical properties, respectively.ConclusionThis study reveals that intercropping tobacco with insectary floral plants, particularly T. erecta, V. villosa, L. maritima and A. frutescens significantly affects soil chemical properties and alters rhizosphere microbial communities, increasing the abundance of certain microbial genera. Additionally, intercropping enhances pathways related to carbohydrate, amino acid, and energy metabolism in rhizosphere bacteria. These findings suggest that intercropping could provide a promising strategy to overcome challenges associated with continuous tobacco cropping by regulating the rhizosphere environment.

Regulation of wheat yield by soil multifunctionality and metagenomic-based microbial degradation potentials under crop rotations

Crop rotation benefits soil fertility and crop yield by providing organic components including cellulose, lignin, chitin, and glucans that are mainly degraded by soil microbial carbohydrate-active enzymes (CAZymes). However, the impacts of crop rotation on soil microbial CAZyme genes are not well understood. Hence, CAZyme genes and families involved in the degradation of differentially originated organic components were investigated using metagenomics among distinct crop rotations. Crop rotation had a more significant effect on soil nitrogen than on carbon fractions with higher content in the complex rotation referring to alfalfa (Medicago sativa L.; 4 year)-potato (Solanum tuberosum L.; 1 year)-winter wheat (3 year; A4PoW3). The composition of soil microbial CAZyme genes related to the degradation of fungi-derived components was more affected by crop rotation compared with the degradation of plant- and bacteria-derived components. The total abundance of CAZyme genes and families was significantly higher in the complex rotation. Notably, CAZyme genes belonging to glycoside hydrolase and glycosyl transferase families had more connections in their network. Moreover, key genes including CE4, GH20, and GH23 assembled toward the middle of the network, and were significantly regulated by dominant soil nitrogen fractions including soil potential nitrogen mineralization and microbial biomass nitrogen. Soil multifunctionality was mostly explained by the composition and total abundance of CAZyme genes, but wheat grain yield was profoundly regulated by fungi-derived components degradation genes under effects of dominant nitrogen fractions. Overall, the findings provide deep insight into the degradation potentials of soil microbial CAZyme genes for developing sustainable crop rotational agroecosystems.

Enhancement of volatile fatty acids to extremely high content in fermentation of food waste: Optimization of conditions, microbial functional genes, and mechanisms

The engineering application of volatile fatty acids (VFA) production from food waste (FW) can significantly enhance resource utilization. Enhancing VFA production is crucial for advancing this engineering application. This study presented a economically-feasible method to achieve high VFA production from FW: Conducting fermentation at pH 9 and 37 ℃ with addition of 20 % anaerobic sludge significantly increased the conversion of FW to VFAs (80.56 g COD/L, accounting for 87.37 % of the soluble chemical oxygen demand), while also increasing the content of NH4+-N (2658.15 mg/L). Macrotranscriptomic sequencing showed that Anaerosalibacter, Amphibacillus, Wansuia, Clostridiisalibacter, unclassified Tissierellia, Massilibacterium, unclassified Bacteroidales, and Tissierellia were the key active microorganisms for VFA production. The expression abundance of functional enzymes and genes related to VFA production pathways increased during the fermentation. This study significantly advanced the practical application of VFA production from FW, offering both theoretical insights and bacterial resources.

Harnessing the microbial interactions from Apocynum venetum phyllosphere for natural product discovery

Natural products (NPs) afforded by living-beings, especially by microscopic species, represent invaluable and indispensable reservoirs for drug leads in clinical practice. With the rapid advancement in sequencing technology and bioinformatics, the ever-increasing number of microbial biosynthetic gene clusters (BGCs) were decrypted, while a great deal of BGCs remain cryptic or inactive under standard laboratory culture conditions. Addressing this dilemma requires innovative tactics to awaken quiescence of BGCs by releasing the potential of microbial secondary metabolism for mining novel NPs. In this study, a universal strategy was proposed to induce the expression of silent BGCs by leveraging the dynamic interactions among coexisting microbial neighbors within a microbiota. This approach involves the deconstruction/reconstruction of binary interactions among the coexisting neighbors to create a pipeline for BGCs arousing. Coupled with the acquisition of 2,760 microbial individuals from the Apocynum venetum (Luobuma, LBM) phyllosphere in a successive dilution procedure, 44 culturable isolates were screened using binary interaction, in which 12.6% pairs demonstrated potent mutual interacting effects. Furthermore, after selecting the most four promising isolates, a full-scale metabolic inspection was conducted, in which 25.3% of the interacting pairs showcased significant metabolomic variations with de-cryptic activities. Notably, with the aid of visualization of IMS technology, one of the physiologically functional entities, the bactericidal agent resistomycin, was elucidated from the core interacting pair between the co-culture of the Streptomyces sp. LBM_605 and the Rhodococcus sp. LBM_791. This study highlights the intrinsic interactions among coexisting microorganisms within a phyllosphere microbiota as novel avenues for exploring and harnessing NPs.

Nitrogen enrichment stimulates nutrient cycling genes of rhizosphere soil bacteria in the Phoebe bournei young plantations

Anthropogenic nitrogen (N) deposition is expected to increase substantially and continuously in terrestrial ecosystems, endangering the balance of N and phosphorus (P) in P-deficient subtropical forest soil. Despite the widely reported responses of the microbial community to simulated N deposition, there is limited understanding of how N deposition affects the rhizosphere soil processes by mediating functional genes and community compositions of soil bacteria. Here, five levels of simulated N deposition treatments (N0, 0 g m−2·yr−1; N1, 100 g m−2·yr−1; N2, 200 g m−2·yr−1; N3, 300 g m−2·yr−1; and N4, 400 g m−2·yr−1) were performed in a 10-year-old Phoebe bournei plantation. Quantitative microbial element cycling smart chip technology and 16S rRNA gene sequencing were employed to analyze functional gene compositions involved in carbon (C), N, and P cycling, as well as rhizosphere bacterial community composition. N deposition significantly influenced C cycling relative abundance of genes in the rhizosphere soil, especially those involved in C degradation. Low and moderate levels (100–300 g m−2·yr−1) of N deposition promoted the relative abundance of the C decomposition-related genes (e.g., amyA, abfA, pgu, chiA, cex, cdh, and glx), whereas high N deposition (400 g m−2·yr−1) suppressed enzyme (e.g., soil invertase, soil urease, and soil acid phosphatase) activities, affecting the C cycling processes in the rhizosphere. Simulated N deposition affected the functional genes associated with C, N, and P cycling by mediating soil pH and macronutrients. These findings provide new insights into the management of soil C sequestration in P. bournei young plantations as well as the regulation of C, N, and P cycling and microbial functions within ecosystems.

The shifts in microbial interactions and gene expression caused by temperature and nutrient loading influence Raphidiopsis raciborskii blooms

Climate change and the trophic status of water bodies are important factors in global occurrence of cyanobacterial blooms. The aim of this study was to explore the cyanobacteria‒bacterial interactions that occur during Raphidiopsis raciborskii (R. raciborskii) blooms by conducting microcosm simulation experiments at different temperatures (20 °C and 30 °C) and with different phosphorus concentrations (0.01 mg/L and 1 mg/L) using an ecological model of microbial behavior and by analyzing microbial self-regulatory strategies using weighted gene coexpression network analysis (WGCNA). Three-way ANOVA revealed significant effects of temperature and phosphorus on the growth of R. raciborskii (P < 0.001). The results of a metagenomics-based analysis of bacterioplankton revealed that the synergistic effects of both climate and trophic changes increased the ability of R. raciborskii to compete with other cyanobacteria for dominance in the cyanobacterial community. The antagonistic effects of climate and nutrient changes favored the occurrence of R. raciborskii blooms, especially in eutrophic waters at approximately 20 °C. The species diversity and richness indices differed between the eutrophication treatment group at 20 °C and the other treatment groups. The symbiotic bacterioplankton network revealed the complexity and stability of the symbiotic bacterioplankton network during blooms and identified the roles of key species in the network. The study also revealed a complex pattern of interactions between cyanobacteria and non-cyanobacteria dominated by altruism, as well as the effects of different behavioral patterns on R. raciborskii bloom occurrence. Furthermore, this study revealed self-regulatory strategies that are used by microbes in response to the dual pressures of temperature and nutrient loading. These results provide important insights into the adaptation of microbial communities in freshwater ecosystems to environmental change and provide useful theoretical support for aquatic environmental management and ecological restoration efforts.

Breed Selection of Poplars Imposes Greater Selection Pressure on the Rhizosphere Bacterial Community

Breed selection alters the coevolution of plant–microbiome associations that have developed over long periods of natural evolution. We investigated the effects of breed selection on the rhizosphere microbiomes and metabolites of hybrid parents (I101 and 84K) and their offspring (Q1–Q5) using metagenomics and untargeted metabolomics. Rhizosphere archaeal, bacterial and fungal community β-diversity significantly differed among hybrid parents and offspring, but only the dominant bacterial phyla and bacterial community α-diversity revealed significant differences. Approximately 5.49%, 14.90% and 7.86% of the archaeal, bacterial and fungal species significantly differed among the poplar hybrid parents and offspring. Rhizosphere microbial functional genes and metabolites were both clustered into the following three groups: I101 and 84K; Q2 and Q4; and Q1, Q3 and Q5. Compared with the hybrid parents, 15 phytochemical compounds were enriched in the hybrid offspring and explained 7.15%, 18.24% and 6.68% of the total variation in the archaeal, bacterial and fungal community compositions, respectively. Rhizosphere metabolites significantly affected the bacterial community, rather than the archaeal and fungal communities. Our observations suggested that poplar breed selection imposed greater selection pressure on the rhizosphere bacterial community, which was mainly driven by metabolites.

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.

Gut microbiota predict retinopathy in patients with diabetes: A longitudinal cohort study

The gut microbiota has emerged as an independent risk factor for diabetes and its complications. This research aimed to delve into the intricate relationship between the gut microbiome and diabetic retinopathy (DR) through a dual approach of cross-sectional and prospective cohort studies. In our cross-sectional study cross-sectional investigation involving ninety-nine individuals with diabetes, distinct microbial signatures associated with DR were identified. Specifically, gut microbiome profiling revealed decreased levels of Butyricicoccus and Ruminococcus torques group, alongside upregulated methanogenesis pathways among DR patients. These individuals concurrently exhibited lower concentrations of short-chain fatty acids in their plasma. Leveraging machine learning models, including random forest classifiers, we constructed a panel of microbial genera and genes that robustly differentiated DR cases. Importantly, these genera also demonstrated significant correlations with dietary patterns and the molecular profiles of peripheral blood mononuclear cells. Building upon these findings, our prospective cohort study followed 62 diabetes patients over a 2-year period to assess the predictive value of these microbial markers. The results underlined the panel’s efficacy in predicting DR incidence. By stratifying patients based on the predictive genera and metabolites identified in the cross-sectional phase, we established significant associations between reduced levels of Butyricicoccus, plasma acetate, and increased susceptibility to DR. This investigation not only deepens our understanding of how gut microbiota influences DR but also underscores the potential of microbial markers as early indicators of disease risk. These insights hold promise for developing targeted interventions aimed at mitigating the impact of diabetic complications.Key points• Microbial signatures are differed in diabetic patients with and without retinopathy• DR-related taxa are linked to dietary habits and transcriptomic profiles• Lower abundances of Butyricicoccus and acetate were prospectively associated with DR

Quantitative Characterization of Gene Regulatory Circuits Associated With Fungal Secondary Metabolism to Discover Novel Natural Products.

Microbial genetic circuits are vital for regulating gene expression and synthesizing bioactive compounds. However, assessing their strength and timing, especially in multicellular fungi, remains challenging. Here, an advanced microfluidic platform is combined with a mathematical model enabling precise characterization of fungal gene regulatory circuits (GRCs) at the single-cell level. Utilizing this platform, the expression intensity and timing of 30 transcription factor-promoter combinations derived from two representative fungal GRCs, using the model fungus Aspergillus nidulans are determined. As a proof of concept, the selected GRC combination is utilized to successfully refactor the biosynthetic pathways of bioactive molecules, precisely control their production, and activate the expression of the silenced biosynthetic gene clusters (BGCs). This study provides insights into microbial gene regulation and highlights the potential of platform in fungal synthetic biology applications and the discovery of novel natural products.

Human gut commensal Alistipes timonensis modulates the host lipidome and delivers anti-inflammatory outer membrane vesicles to suppress colitis in an Il10 -deficient mouse model.

Correlative studies have linked human gut microbes to specific health conditions. Alistipes is one such microbial genus negatively linked to inflammatory bowel disease (IBD). However, the protective role of Alistipes in IBD has not been studied and the underlying molecular mechanisms also remain unknown. In this study, colonization of Il10 -deficient mice with Alistipes timonensis DSM 27924 delays the development of colitis. Colonization with Alistipes does not significantly alter the gut microbiome composition during colitis development, but instead shifts the host plasma lipidome, increasing phosphatidic acids while decreasing triglycerides. Outer membrane vesicles (OMVs) derived from Alistipes are also detected in the plasma of colonized mice, which carry metabolites with immunomodulatory potential into the host circulatory system. We further demonstrate that fractions of A. timonensis OMVs suppress LPS-induced Il6 , Il1b , and Tnfa expression in vitro in murine macrophages. We detect immunomodulatory sulfonolipids (SoLs) in the active fraction, which are also increased in the blood of A. timonensis -colonized mice; and we identify other putative bioactive lipids in the A. timonensis OMVs. Thus, A. timonensis OMVs represent a potential mechanism for Alistipes -mediated delay of colitis progression in Il10 -deficient mice through the delivery of immunomodulatory lipids, including SoLs, and modulation of the host plasma lipidome.

Warm growing season activates microbial nutrient cycling to promote fertilizer nitrogen uptake by maize

The influence of nitrogen (N) inputs on soil microbial communities and N uptake by plants is well-documented. Seasonal variations further impact these microbial communities and their nutrient-cycling functions, particularly within multiple cropping systems. Nevertheless, the combined effects of N fertilization and growing seasons on soil microbial communities and plant N uptake remain ambiguous, thereby constraining our comprehension of the optimal growing season for maximizing crop production. In this study, we employed 15N isotope labeling, high-throughput sequencing, and quantitative polymerase chain reaction (qPCR) techniques to investigate the effects of two distinct growing seasons on microbial communities and maize 15N uptake ratios (15NUR). Our results showed that the warm growing season (26.6 °C) increased microbial diversity, reduced network complexity but enhanced stability, decreased microbial associations, and increased modularization compared to the cool growing season (23.1 °C). Additionally, the warm growing season favored oligotrophic species and increased the abundance of microbial guilds and functional genes related to N, phosphorus, and sulfur cycling. Furthermore, alterations in the characteristics of soil microbial keystone taxa were closely linked to variations in maize 15NUR. Overall, our findings demonstrate significant seasonal variations in soil microbial diversity and functioning, with maize exhibiting higher 15NUR during the warm growing season of the double cropping system.