Microbial Compounds Research Articles

2-Methylbutyric acid functions as a potential antifungal fumigant by inhibiting Botrytis cinerea and inducing resistance to gray mold in cherry tomatoes

Botrytis cinerea causes gray mold disease on postharvest fruit, resulting in serious economic losses. Fumigation with natural volatile organic compounds can replace artificially synthesized fungicides to control postharvest fungal decay of agricultural products. The antifungal effects and potential mechanisms of microbial volatile compound 2-methylbutyric acid (2-MBA) against B. cinerea were investigated in this study. Results showed that 2-MBA inhibited mycelial growth and spores germination, altered mycelial morphology and reduced metabolic vitality of B. cinerea. Moreover, 2-MBA induced oxidative damage by stimulating ROS accumulation, increasing malondialdehyde levels, and decreasing the ratio of reduced/oxidized glutathione. Further studies indicated that 2-MBA reduced mitochondrial membrane potential, interfered TCA cycle by decreasing succinate dehydrogenase activity and ATP content, ultimately leading to decreased mitochondrial activity. In addition, key genes involved in botrydial biosynthesis and mycelial growth were down-regulated. 2-MBA controlled postharvest gray mold by inducing resistance to B. cinerea in cherry tomatoes. Taken together, 2-MBA is an effective and promising fumigant to control gray mold caused by B. cinerea.

Humidity controls soil organic carbon accrual in grassland on the Qinghai–Tibet Plateau

The huge soil organic C (SOC) storage (around 34 Pg in the top 0.7 m) in Qinghai–Tibet Plateau (QTP) grasslands is commonly explained by slow decomposition of litter under cold climate therein, but this view may not be reliable as humidity also affects microbial activity. We sampled the 20 cm topsoil of grasslands along an altitudinal gradient from 1286 m on the western Loess Plateau (LP) to 4200 m above sea level on the northeastern QTP. The light-fraction SOC (LFOC), composition of non-cellulosic neutral carbohydrates, and amino sugars were used as biomarkers to investigate the intensity of microbial action on SOC as a function of climate along this altitudinal gradient. From the lowest-to the highest-humidity site with rising altitude, the root biomass tripled and the SOC content increased approximately sevenfold (from 13.5 g kg−1 to 93.3 g kg−1). The non-cellulosic neutral carbohydrate, microbial biomass C (MBC), and microbial necromass C (MNC) contents increased, but the LFOC content decreased. The contribution of MNC to the SOC and ratios between microbially- and plant-derived sugars in the non-cellulosic carbohydrate pool increased, but the proportion of LFOC in the SOC dropped. Consequently, besides the increased root biomass, the selective preservation of microbial compounds at colder and more humid sites contributed to SOC accruals in grasslands. The higher MBC in cold and humid grasslands perfectly explained the increased selective preservation of microbial derived C at the expense of plant C in higher-relative to lower-altitude areas. Importantly, the above humidity-controlled accumulations of microbial substances and SOC in grasslands were confirmed by results synthesized from published data across the LP and QTP. The higher SOC contents in cold and humid QTP grasslands relative to warm and dry regions were ascribed to the increased accumulation of microbial residues because of the increased humidity in QTP grasslands.

Unraveling the Role of the Human Gut Microbiome in Health and Diseases.

The human gut is a complex ecosystem that supports billions of living species, including bacteria, viruses, archaea, phages, fungi, and unicellular eukaryotes. Bacteria give genes and enzymes for microbial and host-produced compounds, establishing a symbiotic link between the external environment and the host at both the gut and systemic levels. The gut microbiome, which is primarily made up of commensal bacteria, is critical for maintaining the healthy host's immune system, aiding digestion, synthesizing essential nutrients, and protecting against pathogenic bacteria, as well as influencing endocrine, neural, humoral, and immunological functions and metabolic pathways. Qualitative, quantitative, and/or topographic shifts can alter the gut microbiome, resulting in dysbiosis and microbial dysfunction, which can contribute to a variety of noncommunicable illnesses, including hypertension, cardiovascular disease, obesity, diabetes, inflammatory bowel disease, cancer, and irritable bowel syndrome. While most evidence to date is observational and does not establish direct causation, ongoing clinical trials and advanced genomic techniques are steadily enhancing our understanding of these intricate interactions. This review will explore key aspects of the relationship between gut microbiota, eubiosis, and dysbiosis in human health and disease, highlighting emerging strategies for microbiome engineering as potential therapeutic approaches for various conditions.

Microbial community succession patterns and metabolite profiles in cigar tobacco during different mildew stages

Mildew in cigar tobacco leaves (CTLs) degrades both quality and market value. This research systematically examines dynamic changes in key metabolic compounds and microbial community succession throughout the mildew process, categorized into three stages: un-mildew (d0), early-mildew (d4 and d8), and late-mildew (d12 and d16). As mildew progresses, carbohydrates decrease, nitrogen metabolism is hindered, the carbon-nitrogen ratio (C/N) declines, and pH rises, making the tobacco weakly alkaline. The total amount of volatile flavor compounds (VFCs) increases, with the proportion of nitrogen-containing compounds such as nicotine rising, while neophytadiene, ketones, and alcohols decrease, leading to a disruption in the coordination of various aroma substances. Microbial diversity declines, with shifts in populations of Staphylococcus, Pseudomonas, Aspergillus, and Sampaiozyma. Six fungal and five bacterial genera are the characteristic dominate microorganisms at different stages. Co-occurrence network analysis shows that complexity decreases and stability declines, while microbial diversity peaks at the early-mold stage and is severely compromised at the late-mold stage in terms of stability and functional diversity. Two-way Orthogonal Partial Least Squares (O2PLS) identified 12 fungal and 3 bacterial genera as key drivers of metabolic changes. Partial Least Squares Structural Equation Modeling (PLS-SEM) emphasized the role of fungi in CTL degradation and the impact of C/N ratio on fungal metabolism. This study, for the first time, elucidates the complex relationship between microbial succession and metabolite compounds during mildew process, providing a reference for dynamic monitoring of fermented tobacco quality.

Analysis of the association between microbiota and flavor formation during Zizhong Dongjian fermentation process.

Zizhong Dongjian (ZZDJ) is one of the most famous and popular fermented vegetables in China. The aim of this study was to explore the microbial communities and volatile flavor compounds of ZZDJ during different fermentation periods, as well as to reveal the potential correlation between microbiota and flavor. A total of 84 volatile flavor compounds were detected in 0-year to 3-year ZZDJ samples. Hydrocarbons were the most abundant flavor compounds in 0-year and 1-year samples, while esters became the predominant flavor components in 2-year and 3-year samples. Furthermore, Loigolactobacillus, Pseudomonas, and Virgibacillus were most predominant bacteria during the fermentation process of ZZDJ. Interestingly, all the fungi identified were yeasts. Among them, Zygosaccharomyces and Symmetrospora dominated alternatively throughout the fermentation process of ZZDJ. Through analysis of relativity between flavor compounds and microorganism of ZZDJ, we found that Uncultured Pseudomonas sp., Virgibacillus sediminis, Zygosaccharomyces rouxii, and Symmetrospora marina might play important roles in flavor information of ZZDJ.

Dynamic changes in microbial communities and volatile compounds in kombucha fermentation using Flos sophorae and Elm fruits, compared to black and green tea

The dynamic changes in physicochemical properties, microbial communities, and volatile compounds in kombucha made from Flos sophorae (FLSK) and Elm fruit (EFK) were compared to those of black tea (BTK) and green tea (GTK) over a 12-day fermentation period. The results revealed that overall flavonoid and polyphenol content, as well as antioxidant activity, increased initially and then decreased, accompanied by a steady reduction in pH within the fermentation broths investigated. Notably, the GTK exhibited stronger antioxidant activity than the other fermentation broths. Furthermore, 16S rRNA gene sequencing revealed that Komagataeibacter rhaeticus, Komagataeibacter saccharivorans, and Acidovorax wautersii were the dominating microbial species in the fermentation broths under this study. Komagataeibacter rhaeticus initially reduced and then increased throughout the FLSK fermentation, whereas Komagataeibacter saccharivorans increased from day 0 to day 6, and remain stable by day 12 during the EFK fermentation. Comparative analysis revealed that Komagataeibacter rhaeticus was more abundant in the FLSK and GTK than in the EFK and BTK, whereas Komagataeibacter saccharivorans showed a higher abundance in the EFK relative to the other fermentation broths. Gas chromatography-mass spectrometry identified acetic acid, linalool, ethanol, and ethyl acetate as the major volatile chemicals that rose significantly in fermentation mixtures of the examined substrates. The FLSK had a much higher linalool concentration than the other fermentation broths, although the EFK and GTK had higher ethanol content. Correlation study found that Komagataeibacter rhaeticus was negatively related with alcohol compounds, but Komagataeibacter saccharivorans was positively associated with a diverse spectrum of acids, alcohols, and esters. The study found changes in bioactive chemicals as well as interactions between bacterial populations and volatile compounds throughout fermentation in the substrates investigated.

Dynamic Changes and Potential Correlations between Microbial Diversity and Volatile Flavor Compounds in Chinese Medium-Temperature Daqu during Manufacturing.

To investigate the dynamic changes and potential correlations between microbial diversity and volatile organic compounds (VOCs) during Chinese medium-temperature Daqu (MTD) manufacturing at different key stages, in this study, high-throughput sequencing (HTS) and gas chromatography-ion mobility spectrometry (GC-IMS) were employed to analyze the microbial diversity and VOCs of MTD, respectively. The results showed that Weissella, Staphylococcus, Thermoactinomyces, Kroppenstedtia, and Lactobacillus were the dominant bacterial genera, while Aspergillus, Alternaria, Thermoascus, Thermomyces, Wickerhamomyces, and Saccharomyces were the dominant fungal genera. A total of 61 VOCs were detected by GC-IMS, among which, 13 differential VOCs (VIP > 1) were identified, that could be used as potential biomarkers to judge the fermentation stage of MTD. Kroppenstedtia and Saccharopolyspora were positively correlated with 3-methyl-2-butenal and 2,2,4,6,6-pentamethylheptane-D, respectively, and both of these were positively correlated with butanal-D. Acetobacter, Streptomyces, and lactic acid bacteria (LAB) including Leuconostoc, Pediococcus, Weissella, and Lactobacillus were negatively correlated with their associated VOCs, while fungi were generally positively correlated with VOCs. Wickerhamomyces, Saccharomyces, and Candida were positively correlated with butan-2-one-M. This study provides a theoretical basis for explaining the mechanisms of MTD flavor formation and screening functional microorganisms to improve the quality of MTD.

The Gut Microbiome in Sepsis: From Dysbiosis to Personalized Therapy

Sepsis is a complex clinical syndrome characterized by an uncontrolled inflammatory response to an infection that may result in septic shock and death. Recent research has revealed a crucial link between sepsis and alterations in the gut microbiota, showing that the microbiome could serve an essential function in its pathogenesis and prognosis. In sepsis, the gut microbiota undergoes significant dysbiosis, transitioning from a beneficial commensal flora to a predominance of pathobionts. This transformation can lead to a dysfunction of the intestinal barrier, compromising the host’s immune response, which contributes to the severity of the disease. The gut microbiota is an intricate system of protozoa, fungi, bacteria, and viruses that are essential for maintaining immunity and metabolic balance. In sepsis, there is a reduction in microbial heterogeneity and a predominance of pathogenic bacteria, such as proteobacteria, which can exacerbate inflammation and negatively influence clinical outcomes. Microbial compounds, such as short-chain fatty acids (SCFAs), perform a crucial task in modulating the inflammatory response and maintaining intestinal barrier function. However, the role of other microbiota components, such as viruses and fungi, in sepsis remains unclear. Innovative therapeutic strategies aim to modulate the gut microbiota to improve the management of sepsis. These include selective digestive decontamination (SDD), probiotics, prebiotics, synbiotics, postbiotics, and fecal microbiota transplantation (FMT), all of which have shown potential, although variable, results. The future of sepsis management could benefit greatly from personalized treatment based on the microbiota. Rapid and easy-to-implement tests to assess microbiome profiles and metabolites associated with sepsis could revolutionize the disease’s diagnosis and management. These approaches could not only improve patient prognosis but also reduce dependence on antibiotic therapies and promote more targeted and sustainable treatment strategies. Nevertheless, there is still limited clarity regarding the ideal composition of the microbiota, which should be further characterized in the near future. Similarly, the benefits of therapeutic approaches should be validated through additional studies.

Temporal heterogeneity of microbial communities and flavor metabolism during storage of high-temperature Daqu

Storage is a crucial step in the production of Daqu, but the microbiological and flavor chemical kinetics of the storage process remain largely unknown and limit the quality control of Daqu. In this study, the microbial communities and volatile compounds were analyzed and compared during the storage of Daqu. Virgibacillus, Bacillus and Kroppenstedtia were the dominant bacterial genera, and Thermoascus, Thermomyces and Aspergillus were the dominant fungal genera. By LEfSe analysis, JW1 Daqu had more differential microbial markers. At the end of storage, the content of some compounds decreased significantly, such as esters, alcohols and ketones. In addition, PICRUSt2 predicted enzymes related to some important aroma production. These results indicated that microbial communities and volatiles changed significantly during storage of Daqu, which might be important for optimization of quality.

Drosophila suzukii and Drosophila melanogaster prefer distinct microbial and plant aroma compounds in a complex fermented matrix

Volatile aroma compounds are important chemical cues for insects. Behavioral responses to specific odors differ strongly between insect species, and the exact causative molecules are often unknown. Beer is frequently used in insect traps because it combines hundreds of plant and microbial aromas that attract many insects. Here, we analyzed responses of the pest fruit fly Drosophila suzukii and benign Drosophila melanogaster to beers with different chemical compositions. Using extensive chemical and behavioral assays, we identified ecologically relevant chemicals that influence drosophilid behavior and that induce different odor-evoked activity patterns in the antennal lobe of the two species obtained by functional imaging. Specific mixes of compounds increased the species-specificity and sex-specificity of lures in both laboratory and greenhouse settings. Together, our study shows how examining insect responses to highly complex natural mixtures of aroma compounds provides insight into insect-specific behavioral responses and also opens avenues for improved pest control.

Behavioral responses of predatory flies of the genus Medetera Fischer von Waldheim (Diptera: Dolichopodidae) and the tree-killing beetle Ips typographus L. (Coleoptera: Scolytinae) to odor compound blends

Key MessageMedetera (Fischer von Waldheim) flies, natural enemies of the spruce bark beetle Ips typographus (L.), were attracted to synthetic blends of compounds produced by infested spruce trees. A subset of trapped specimens revealed sixteen Medetera species. Most abundant were M. signaticornis, M. infumata, and M. prjachinae. Only blends containing beetle-produced compounds significantly attracted Medetera spp. and I. typographus.ContextFly species of the genus Medetera (Fischer von Waldheim) (Diptera: Dolichopodidae) represent one of the most important groups of natural enemies of the Eurasian bark beetle Ips typographus (L.), which infests Norway spruce Picea abies (L.) Karst. In a previous study, we showed that adult Medetera flies exploit semiochemicals to find beetle-infested trees however, the exact nature of those attractive compounds has not yet been determined.AimsThe aim of this follow-up study was to investigate the behavioral responses of Medetera spp. and I. typographus, to different combinations of semiochemicals.MethodsIn this study, 22 volatile compounds identified from I. typographus-infested Norway spruce were divided into five groups (A–E) based on being primarily produced by the bark beetle I. typographus (group A), bark beetle-associated microorganisms (groups B and C), or spruce tree (groups D and E). The effect of the compounds in these groups in the attraction of Medetera species and I. typographus was tested in two different subtractive field trapping assays.ResultsIn the first subtractive assay, the full blend (ABCDE), and the blends lacking microbial compounds of group C, or spruce tree compounds of group D led to significant attraction of Medetera flies. Morphological identification of a subset of the specimens collected revealed that sixteen species were attracted to the synthetic blends, with M. signaticornis Loew being the most abundant. In the second subtractive assay, high attraction of Medetera flies and I. typographus was found for a 12-component synthetic blend.ConclusionThe insights gained provide a basis for developing synthetic attractants to facilitate monitoring of Medetera flies. Future testing and optimization of these attractants will enhance our ability to monitor, conserve and utilize Medetera flies, thereby enabling us to better protect forests from the damaging effects of spruce bark beetles.

Secondary metabolites with antimicrobial activity produced by thermophilic bacteria from a high-altitude hydrothermal system.

Thermophilic microorganisms possess several adaptations to thrive in high temperature, which is reflected as biosynthesis of proteins and thermostable molecules, isolation and culture represent a great methodological challenge, therefore High throughput sequencing enables screening of the whole bacterial genome for functional potential, providing rapid and cost-effective information to guide targeted cultures for the identification and characterization of novel natural products. In this study, we isolated two thermophilic bacterial strains corresponding to Bacillus LB7 and Streptomyces LB8, from the microbial mats in the Atacama Desert. By combining genome mining, targeted cultures and biochemical characterization, we aimed to identify their capacity to synthesize bioactive compounds with antimicrobial properties. Additionally, we determined the capability to produce bioactive compounds under controlled in vitro assays and detected by determining their masses by Thin-Layer Chromatography/Mass Spectrometry (TLC/MS). Overall, both isolates can produce antimicrobial (e.g., Myxalamide C by-product) and antioxidants (e.g. Dihydroxymandelic Acid, Amide biotine and Flavone by-products) compounds. Bacillus LB7 strain possesses a more diverse repertoire with 51.95% of total metabolites unmatched, while Streptomyces LB8 favors mainly antioxidants, but has over 70% of unclassified compounds, highlighting the necessity to study and elucidate the structure of novel compounds. Based on these results, we postulate that the uncultured or rare cultured thermophiles inhabiting high-altitude hydrothermal ecosystems in the Atacama Desert offer a promising opportunity to the study of novel microbial bioactive compounds.

The Role of Gut Microbiota as a Trigger for Exacerbations in Pulmonary Obstruction Disorder in General

Pulmonary diseases can be associated with the gastrointestinal (GI) system, particularly if an infection causes them. This relationship between organs is known as the gut-lung axis (GLA). Skin and mucosal surfaces are associated with microbiota (bacteria, fungi, viruses, macrophages, archaea, protists, helminths), which can trigger an immune response in GLA and serve a role in respiratory diseases. For instance, asthma can be inhibited by a specific antigen that is triggered by probiotics, the microorganisms found in the GI tract. Asthma incidence can be reduced by consuming fiber due to its ability to protect airways from infection. Pattern recognition receptors (PRRs) are the first immune component to identify microbial compounds in GI and lung epithelial cells. The PRRs then induce regulatory T-cell (T-reg) and Th-17 differentiation. Diet, antibiotics, and stress can all influence the structure and function of bacteria. This is known as dysbiosis. Lung microbiota can influence immune cell maturation and homeostasis. If the diversity of lung microbiota decreases, it will affect intestinal microbiota and may result in chronic respiratory disorders such as chronic obstructive pulmonary disease (COPD), asthma, and cystic fibrosis. This literature review explained how the interactions between the intestines and lungs can affect humans’ health and well-being.

Effect of temperature on the quality and microbial community during Daocai fermentation

Daocai is a traditional salted pickle in the southeastern region of Guizhou with a unique aroma, color, and taste. The quality of Daocai is greatly influenced by the fermentation temperature. In this study, high-throughput sequencing and headspace-gas chromatography-ion mobility spectrometry were used to investigate the changes in microbial community succession and volatile flavor compounds during Daocai fermentation under temperature-controlled (D group) and non-temperature-controlled (C group).We found that the predominant genera in the C group samples were Latilactobacillus(40.57 %), Leuconostoc(21.25 %), Cystofilobasidium(22.12 %), Vishniacozyma(23.89 %), and Leucosporidium(24.95 %), whereas Weissella(29.39 %), Lactiplantibacillus(45.61 %), Mucor(68.26 %), and Saccharomyces(23.94 %) were the predominant genera in the D group. A total of 92 VFCs were detected in Daocai samples, including 5 isothiocyanates, 16 esters, 14 alcohols, 24 aldehydes, 17 ketones, 3 acids, 2 pyrazines, 1 pyridines, 1 thiazoles, 3 furans, 4 alkenes, and 2 nitriles. Further analysis revealed Latilactobacillus, Leuconostoc, Lactococcus, Cystofilobasidium, Leucosporidium, Holtermanniella, and Dioszegia as key bacteria involved in flavor formation. They are closely related to the formation of flavors such as aldehydes, furans, pyridines, and alkenes. This study contributes to our understanding of the relationship between bacterial communities and the flavor formation during Daocai fermentation.

Interaction and dynamic changes of microbial communities and volatile flavor compounds during the fermentation process of coffee flower rice wine.

To develop a unique flavor of rice wine, coffee flowers (by-products of the coffee industry) were added because of their biologically active compounds that are conducive to health, and the fermentation parameters were optimized. In addition, the dynamic changes of microbial communities and volatile flavor compounds (VFCs) during the different fermentation stages were investigated. After the optimization of the fermentation parameters, a novel product, i.e., the coffee flower rice wine (CFRW), was obtained with a bright yellow transparent, fragrant, and harmonious aroma and mellow and refreshing taste by sensory evaluation, when 4.62% of the coffee flowers and 1.93% koji were added and fermented at 24.10°C for 3.88 days. The results showed that Lactococcus was the dominant bacteria, accounting for 87.0-95.7%, while Rhizopus and Cladosporium were the main fungi, accounting for 68.2% and 11.3% on average, respectively, in the fermentation process of the CFRW. Meanwhile, twenty-three VFCs were detected in the CFRW, which included three alcohols, six terpenes, ten esters, three aromatics, and one furan. The correlation analysis revealed that there were 16 significant positive correlations and 23 significant negative correlations between the bacterium and VFCs (|ρ| > 0.6, p < 0.05), while there were 12 significant positive correlations and one significant negative correlation between the fungi and VFCs (|ρ| > 0.6, p < 0.05). Furthermore, five VFCs, including linalool, geraniol, ethyl acetate, 1-hexanol, and 3-methyl-1-butanol, contributed vital flavors to the CFRW, and they were all significantly negatively correlated with the changes of Massilia and Acinetobacter (|ρ| > 0.6, p < 0.05). Moreover a significant positive correlation was found between the relative abundance of Lactococcus and the contents of 3-methyl-1-butanol and ethyl acetate (|ρ| > 0.6, p < 0.05). Therefore, this study provides a valuable theoretical basis for further improving the quality and production technology of CFRW.

Production of secondary metabolites by Actinomycetes and their biological applications: A review

Bioactive metabolites are a substance that has a biological activity and should include all microbial compounds obtained either from microbes or from any other living thing. Around 23,000 bioactive metabolites produced from microorganisms, out of which 10,000 (45%) are produced by Actinobacteria alone. Actinomycetes are known to produce an extensive range of bioactive metabolites as well as variety of enzymes with multiple biotechnological applications and important for pharmaceutical, food, agricultural, and environmental applications. Bioactive metabolites are widely used and studied for obtaining antibiotics, antifungals, antivirals, immunosuppressants, compounds with anticancer and antioxidant activity, enzymes, bioinsecticides, biostimulants, biosurfactants and other applications. Bioactive metabolites derived from Actinomycetes are more attractive than bioactive metabolites from other sources because of their high stability and unusual activity specificity. The main applications of Actinomycetes, studies have focused on antimicrobial potential, enzymes production, agricultural uses, bioremediation, and others related to their secondary metabolites production. The review aimed to summarize information about the potentials of Actinomycetes novel bioactive metabolites with their applications in different prospects.

The impacts of ecological disturbances on the diversity of biosynthetic gene clusters in kauri (Agathis australis) soil

BackgroundThe ancient kauri (Agathis australis) dominated forests of Aotearoa New Zealand are under threat from a multitude of ecological disturbances such as forest fragmentation, biodiversity loss, climate change, and the spread of the virulent soil pathogen Phytophthora agathidicida. Taking a wider ecosystem-level approach, our research aimed to explore the impacts of forest disturbance and disease outbreaks on the biosynthetic potential and taxonomic diversity of the kauri soil microbiome. We explored the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in soils from a range of kauri forests that varied according to historical disturbance and dieback expression. To characterise the diversity of microbial BGCs, we targeted the non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene regions for sequencing using long-read PacBio® HiFi sequencing. Furthermore, the soil bacterial and fungal communities of each forest were characterized using 16 S rRNA and ITS gene region sequencing.ResultsWe identified a diverse array of naturally occurring microbial BGCs in the kauri forest soils, which may offer promising targets for the exploration of secondary metabolites with anti-microbial activity against P. agathidicida. We detected differences in the number and diversity of microbial BGCs according to forest disturbance history. Notably, soils associated with the most undisturbed kauri forest had a higher number and diversity of microbial NRPS-type BGCs, which may serve as a potential indicator of natural levels of microbiome resistance to pathogen invasion.ConclusionsBy linking patterns in microbial biosynthetic diversity to forest disturbance history, this research highlights the need for us to consider the influence of ecological disturbances in potentially predisposing forests to disease by impacting the wider health of forest soil ecosystems. Furthermore, by identifying the range of microbial BGCs present at a naturally high abundance in kauri soils, this research contributes to the future discovery of natural microbial compounds that may potentially enhance the disease resilience of kauri forests. The methodological approaches used in this study highlight the value of moving beyond a taxonomic lens when examining the response of microbial communities to ecosystem disturbance and the need to develop more functional measures of microbial community resilience to invasive plant pathogens.

Development of oriented microbial consortium-based compound enzyme strengthens food waste hydrolysis and antibiotic resistance genes removal: Deciphering of performance, metabolic pathways and microbial communities

Enzymatic hydrolysis has been considered as an eco-friendly pretreatment method for enhancing bioconversion process of food waste (FW). However, existing commercial enzymes and microbial monomer-based compound enzymes (MME) have the issues of uneven distribution of enzymatic activity and low matching degree with the components of FW, leading to low efficiency with enzymatic hydrolysis and removal of antibiotic resistance genes (ARGs). This study used FW as the substrate, under the co-culture system, produced a microbial consortium-based compound enzymes (MCE) with oriented and well-matching degree for FW hydrolysis and ARGs removal, of which the performance, metabolic pathways and microbial communities were also investigated in depth. Results showed that the best performance for ARGs was achieved by the MCE prepared by mixing 1:5 of Aspergillus oryzae and Aspergillus niger after 12 days fermentation. The highest soluble chemical oxygen demand (SCOD) concentration and ARGs removal could respectively reach 83.90 ± 1.67 g/L and 45.95% after MCE pretreatment. The analysis of metabolic pathways revealed that 1:5 MCE pretreatment strengthened the catalytic activity of carbohydrate-active enzymes, increased the abundances of genes involved in cellulose and starch degradation, polysaccharide synthesis, ATP binding cassette (ABC) transporters and global regulation, while decreased the abundances of genes involved in mating pair formation system, two-component regulatory systems and quorum sensing, thereby enhanced FW hydrolysis and restrained ARGs dissemination. Microbial community analysis further indicated that the 1:5 MCE pretreatment promoted growth, metabolism and richness of functional microbes, while inhibited the host microbes of ARGs. It is expected that this study can provide useful insights into understanding the fate of ARGs in food waste during MCE pretreatment process.

The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches.

In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a "living sponge," taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.

Analysis of the microbial community structure and characteristic flavor of traditional fermented bean paste.

Bean paste is a traditional Chinese fermented condiment, which is loved by consumers for its pleasant flavor and nutritional properties. However, the microbial communities and related flavor compounds in bean paste remain unclear. We studied the correlation between the core functional microorganisms and flavor compounds in bean paste samples at different fermentation stages. Bacterial and fungal communities changed significantly during fermentation. The results indicated that the dominant bacterial genera were Staphylococcus, Lactococcus, and Bacillus. The dominant fungi were Aspergillus and Lichtheimia. During the early and late stages of bean paste fermentation, alcohols, hydrocarbons, esters, and phenols were the main flavor compounds detected. The types and proportions of alcohols and esters in the bean pastes fermented for different durations were similar, whereas the relative contents of phenols and hydrocarbons were higher in the later stages of fermentation. Correlation analysis revealed that core functional microorganisms played a key role in the fermentation process, and the potential correlation between bacterial genera and flavors was stronger than that of fungal genera. Staphylococcus abundance was significantly correlated with the flavor levels of ethyl oleate, ç-pinene, diallyl disulfide, á-myrcene, D-limonene, and tetradecanoic acid, ethyl ester. The abundance of Aspergillus and Lichtheimia was significantly correlated with the flavor levels of á-myrcene, ç-pinene, and DL-3-phenyllactic acid. This study explored the relationship between microorganisms and flavor compounds in bean paste to deepen our understanding of the mechanism of flavor formation for bean paste.