Metatranscriptomics—gene express profiling via DNA sequencing—is a powerful tool to identify genes that are actively expressed and might contribute to the phenotype of individual organisms or the phenome (the sum of...Metatranscriptomics—gene express profiling via DNA sequencing—is a powerful tool to identify genes that are actively expressed and might contribute to the phenotype of individual organisms or the phenome (the sum of several phenotypes) of a microbial community. Furthermore, metatranscriptome studies can result in extensive catalogues of genes that encode for enzymes of industrial relevance. In both cases, a major challenge for generating a high quality metatranscriptome is the extreme lability of RNA and its susceptibility to ubiquitous RNAses. The microbial community (the microbiome) of the cow rumen efficiently degrades lignocelullosic biomass, generates significant amounts of methane, a greenhouse gas twenty times more potent than carbon dioxide, and is of general importance for the physiological wellbeing of the host animal. Metatranscriptomes of the rumen microbiome from animals kept under different conditions and from various types of rumen-incubated biomass can be expected to provide new insights into these highly interesting phenotypes and subsequently provide the framework for an enhanced understanding of this socioeconomically important ecosystem. The ability to isolate large amounts of intact RNA will significantly facilitate accurate transcript annotation and expression profiling. Here we report a method that combines mechanical disruption with chemical homogenization of the sample material and consistently yields 1 mg of intact RNA from 1 g of rumen-incubated biofuel feedstock. The yield of total RNA obtained with our method exceeds the RNA yield achieved with previously reported isolation techniques, which renders RNA isolated with the method presented here as an ideal starting material for metatranscriptomic analyses and other molecular biology applications that require significant amounts of starting material.展开更多
Microbial aggregates of different sizes in aerobic granular sludge(AGS)systems have been shown to exhibit distinct microbial community compositions.However,studies comparing the microbial activities of different-sized...Microbial aggregates of different sizes in aerobic granular sludge(AGS)systems have been shown to exhibit distinct microbial community compositions.However,studies comparing the microbial activities of different-sized aggregates in AGS systems remain limited.In this study,genome-resolved metatranscriptomics was used to investigate microbial activity patterns within differently sized aggregates in a full-scale AGS plant.Our analysis revealed a weak correlation between the relative abundance of metagenome-assembled genomes(MAGs)and their transcriptomic activity,indicating that microbial abundance does not directly correspond to metabolic activity within the system.Flocculent sludge(FL;<0.2 mm)predominantly featured active nitrifiers and fermentative polyphosphate-accumulating organisms(PAOs)from Candidatus Phosphoribacter,while small granules(SG;0.2e1.0 mm)and large granules(LG;>1.0 mm)hosted more metabolically active PAOs affiliated with Ca.Accumulibacter.Differential gene expression analysis further supported these findings,demonstrating significantly higher expression levels of key phosphorus uptake genes associated with Ca.Accumulibacter in granular sludge(SG and LG)compared to flocculent sludge.Conversely,Ca.Phosphoribacter showed higher expression of these genes in the FL fraction.This study highlights distinct functional roles and metabolic activities of crucial microbial communities depending on aggregate size within AGS systems,offering new insights into optimizing wastewater treatment processes.展开更多
In this study,the changes of flavor profile,the succession rules of active microorganisms and their correlation were analyzed during the fermentation process of industrial Sichuan radish paocai,in order to further exp...In this study,the changes of flavor profile,the succession rules of active microorganisms and their correlation were analyzed during the fermentation process of industrial Sichuan radish paocai,in order to further explore the composition of ingredients that constitute the unique flavor characteristics of industrial Sichuan radish paocai,and the microorganisms and enzymes that may contribution to it.To this end,molecular sensory,high performance liquid chromatography and metatranscriptomics were employed to identify the aroma-active compounds,non-volatile compounds and active microorganisms during the 197-day fermentation process of industrial Sichuan radish paocai,respectively.Twenty aroma-active compounds were identified,of which 12 compounds had odor activity values≥1,and some off-flavor compounds were significantly lower than those of fresh radish.After 100 days of fermentation,aroma-active compounds began to accumulate extensively with the dominant active microorganisms transforming from fungi to bacteria.Among the potential formation pathways of 14 aroma-active compounds,most of which were dominated by Lactobacillus and Debaryomyces,and were contributed by other microorganisms mainly belong to Lactobacillales,Saccharomycetales and Bacillales.This study provides new insights into the flavor formation and microbial metabolic roles of industrialized paocai,as well as valuable references for screening and isolation of functional strains,expression and characterization of flavor enzymes.展开更多
Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their meta...Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their metabolic responses to the prevailing environmental conditions.The double-RNA approach involves the simultaneous analysis of rRNA and mRNA,also termed structural and functional metatranscriptomics.By contrast,mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles,but requires either deep sequencing or effective rRNA depletion.In this review,we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional metatranscriptomics.In particular,we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields,such as rhizobiomes,antibiotic resistomes,methanomes,and viromes.Our review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.展开更多
3-Methylindole(skatole)is regarded as one of the most offensive compounds in odor emission.Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain...3-Methylindole(skatole)is regarded as one of the most offensive compounds in odor emission.Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic.In this study,an efficient aerobic skatole-degrading consortium was obtained.Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses.Bioinformatic analyses indicated that the skatole downstream degradation wasmainly via the catechol pathway,and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase.Genome binning and gene analyses indicated that Pseudomonas,Pseudoclavibacter,and Raineyella should cooperate with Rhodococcus for the skatole degradation process.Moreover,a pure strain Rhodococcus sp.DMU1 was successfully obtained which could utilize skatole as the sole carbon source.Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium.Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway.Collectively,our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader,and the degradation mainly proceeded via the catechol pathway.展开更多
Laotan Suancai is a popular traditional Chinese fermented vegetable with a unique flavor.Current studies have focused on revealing the relationship between microbiota and flavor.However,the metabolism of biogenic amin...Laotan Suancai is a popular traditional Chinese fermented vegetable with a unique flavor.Current studies have focused on revealing the relationship between microbiota and flavor.However,the metabolism of biogenic amines(BAs),an important harmful substance,by the microbiota during Laotan Suancai fermentation remains unclear.In this study,we investigated the dynamic changes of eight BAs during the fermentation.The primary BAs,putrescine and cadaverine,reached 45.96±3.01 mg/kg and 43.10±2.37 mg/kg,respectively,at the end of fermentation.Spearman correlation analysis revealed significant correlations between BAs and 15 different species.Besides,the metabolic pathways of BAs were reconstructed via metatranscriptome and metabolome analyses.BAs.Furthermore,key microbes involved in BA metabolism in Laotan Suancai,such as Lactobacillaceae species,Picha,and Tetragenococcus halophilus,were identified.These findings improve our understanding of BA metabolism in fermented vegetables and have implications for the development of starter cultures with the ability to degrade BAs in the industrial production of Laotan Suancai.展开更多
Suansun is a naturally fermented vegetable with unique flavor that depends on metabolic activities of microbiota.However,the formation mechanism of the key flavor driven by active microbiota during suansun fermentatio...Suansun is a naturally fermented vegetable with unique flavor that depends on metabolic activities of microbiota.However,the formation mechanism of the key flavor driven by active microbiota during suansun fermentation is unclear.In this study,metatranscriptomics and metabolomics were used to analyze the key flavor profiles as well as the core functional microorganisms for flavor formation.HS-SPME-GC-MS and UPLC-Q-TOF/MS identified that organic acids,esters,alcohols,aldehydes,phenols and small peptides exert an important influence on the flavor formation of suansun.Based on the metatranscriptomic data,the metabolic network related to the formation of key flavors of suansun was reconstructed.Functional annotation further indicated that 5 genera(including Lactococcus,Enterococcus,Leuconostoc,Lactiplantibacillus and Weissella),which can actively produce enzymes that related to flavor synthesis,were the core functional microorganisms for flavor formation of suansun.These findings contributed to a better understanding of the flavor formation mechanism in suansun and other naturally-fermented foods.展开更多
The human gut microbiome has primarily been studied through the use of fecal samples,a practice that has generated vital knowledge on the composition and functional capacities of gastrointestinal microbial communities...The human gut microbiome has primarily been studied through the use of fecal samples,a practice that has generated vital knowledge on the composition and functional capacities of gastrointestinal microbial communities.However,this reliance on fecal materials limits the investigation of microbial dynamics in other locations along the gastrointestinal tract(in situ),and the infrequent availability of fecal samples prevents analysis at finer temporal scales(e.g.,hours).In our study,we utilized colonic transendoscopic enteral tubing,a technology originally developed for fecal microbiota transplantation,to sample the ileocecal microbiome twice daily;metagenomic and metatranscriptomic analyses were then conducted on these samples.A total of 43 ileocecal and 28 urine and fecal samples were collected from five healthy volunteers.The ileocecal and fecal microbiomes,as profiled in the five volunteers,were found to be similar in metagenomic profiling,yet their active genes(metatranscriptome)were found to be highly distinct.Both microbiomes were perturbed after laxative exposure;over time,they exhibited reduced dissimilarity to their pre-treatment state,thereby demonstrating resilience as an innate property of the gut microbiome,although they did not fully recover within our observation time window.Sampling of the ileocecal microbiome during the day and at night revealed the existence of diurnal rhythms in a series of bacterial species and functional pathways,particularly those related to short-chain fatty acid production,such as Propionibacterium acnes and coenzyme A biosynthesis Ⅱ.Autocorrelation analysis and fluctuations decomposition further indicated the significant periodicity of the diurnal oscillations.Metabolomic profiling in the fecal and urine samples mirrored the perturbance and recovery in the gut microbiome,indicating the crucial contribution of the gut microbiome to many key metabolites involved in host health.This study provides novel insights into the human gut microbiome and its inner resilience and diurnal rhythms,as well as the potential consequences of these to the host.展开更多
Glycogen accumulating organisms(GAOs) are closely related to the deterioration of enhanced biological phosphorus removal systems. However, the metabolic mechanisms that drive GAOs remain unclear. Here, the two-thirds ...Glycogen accumulating organisms(GAOs) are closely related to the deterioration of enhanced biological phosphorus removal systems. However, the metabolic mechanisms that drive GAOs remain unclear. Here, the two-thirds supernatant of a reactor were decanted following the anaerobic period to enrich GAOs. Long-term monitoring demonstrated that the system was stable and exhibited typical characteristics of GAOs metabolism. Acetate was completely consumed after 60 min of the anaerobic phase. The level of glycogen decreased from 0.20 to 0.14 g/gSS during the anaerobic phase, whereas the level of glycogen significantly increased to 0.21g/gSS at the end of the aerobic period. Moreover, there was almost no phosphate release and absorption in the complete periods, thus confirming the successful construction of a GAOs enrichment system. Microbial community analysis demonstrated that Ca. Contendobacter was among the core functional genera and showed the highest activity among all of the communities. Furthermore, our study is the first to identify the involvement of the ethyl-malonyl-CoA pathway in the synthesis of polyhydroxyvalerate via croR, ccr, ecm, mcd, mch and mcl genes. The Embden-Meyerhof-Parnas(EMP) pathway was preferentially used via glgP. Furthermore, the glyoxylate cycle was the main source of ATP under anaerobic conditions, whereas the tricarboxylic acid cycle provided ATP under aerobic conditions. aceA and mdh appeared to be major modulators of the glyoxylate pathway for controlling energy flow. Collectively, our findings not only revealed the crucial metabolic mechanisms in a GAOs enrichment system but also provided insights into the potential application of Ca. Contendobacter for wastewater treatment.展开更多
BACKGROUND Fecal microbiota transplantation(FMT)is a promising therapeutic approach for treating Crohn’s disease(CD).The new method of FMT,based on the automatic washing process,was named as washed microbiota transpl...BACKGROUND Fecal microbiota transplantation(FMT)is a promising therapeutic approach for treating Crohn’s disease(CD).The new method of FMT,based on the automatic washing process,was named as washed microbiota transplantation(WMT).Most existing studies have focused on observing the clinical phenomena.However,the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome,metatranscriptome,and metabolome-has not yet been reported.AIM To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.METHODS We conducted a prospective,open-label,single-center clinical study.Eleven CD patients underwent WMT.Their clinical responses(defined as a decrease in their CD Activity Index score of>100 points)and their microbiome(metagenome,metatranscriptome)and metabolome profiles were evaluated three months after the procedure.RESULTS Seven of the 11 patients(63.6%)showed an optimal clinical response three months post-WMT.Gut microbiome diversity significantly increased after WMT,consistent with improved clinical symptoms.Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains,such as Faecalibac-terium prausnitzii,Roseburia intestinalis,and Escherichia coli.In addition,metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors.However,levels of vital amino acids that may be associated with disease progression(e.g.,L-glutamic acid,gamma-glutamyl-leucine,and prolyl-glutamine)were reduced after WMT.CONCLUSION WMT demonstrated therapeutic efficacy in CD treatment,likely due to the effective reconstruction of the patient’s microbiome.Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.展开更多
Phytoplankton play a vital role in nutrient biogeochemical cycling,and their elemental ratios covary with available inorganic nutrients;however,the underlying interaction patterns and mechanisms remain unclear.Here,ba...Phytoplankton play a vital role in nutrient biogeochemical cycling,and their elemental ratios covary with available inorganic nutrients;however,the underlying interaction patterns and mechanisms remain unclear.Here,based on large-scale and long-term field surveys together with culture experiments,we found a stoichiometric convergence over time between phytoplankton nitrogen(N)∶carbon(C)molar ratios and dissolved inorganic N∶CO_(2)molar ratios.Functional genomics evidence demonstrated that this N-C stoichiometric convergence was driven by phytoplankton community succession with its matched N and C metabolism.A theoretical framework was proposed and proved applicable for depicting this convergence.The convergence speed was faster with the greater difference between phytoplankton and water N∶C molar ratios.Moreover,replacing CO_(2)with dissolved inorganic C could alter the direction of convergence.This stoichiometric convergence characterizes the response of phytoplankton elemental ratios to inorganic nutrient dynamics and represents an evolutionary pathway for phytoplankton community assembly over time.展开更多
Moisture plays a pivotal role in solid-state fermentation by providing essential environmental support for microbial growth,regulating temperature and humidity,influencing metabolic efficiency,and ultimately controlli...Moisture plays a pivotal role in solid-state fermentation by providing essential environmental support for microbial growth,regulating temperature and humidity,influencing metabolic efficiency,and ultimately controlling the fermentation process.This study investigated the effects of moisture on microbial community diversity,functional microorganisms,and metabolic capacity during Daqu fermentation.A room environment monitoring system was developed to collect real-time environmental parameters,revealing moisture as a key driver of microbial community succession(p=0.001).Characteristic microorganisms,including Lichtheimia,Lactiplantibacillus,Pichia,Aspergillus,and Proteus,were identified.Structural equation modeling(SEM)analysis demonstrated that microbialα-diversity exhibited a significant positive correlation with moisture(p<0.01).While increased microbialα-diversity suppressed Lichtheimia and Aspergillus(p<0.05),it significantly promoted the proliferation of Lactiplantibacillus,Pichia,and Proteus(p<0.01).Lichtheimia showed a positive correlation with saccharifying power(p<0.05)and a highly significant positive correlation with esterifying power(p<0.01).The growth of Aspergillus significantly enhanced both saccharifying and liquefying powers of Daqu(p<0.01),whereas Lactiplantibacillus,Pichia,and Proteus markedly improved fermenting power(p<0.01).Metatranscriptomic analysis revealed the expression of key functional enzymes and their microbial origins,demonstrating that Lactiplantibacillus,Pichia,and Wickerhamomyces all contributed to saccharification,liquefaction,fermentation,and esterification.These findings provide both theoretical and practical insights into the influence of moisture on microbial metabolism and the optimization of fermentation processes.展开更多
Excessive levels of higher alcohols have negative impacts on the quality of Baijiu.Understanding the key mi-croorganisms responsible for producing higher alcohols and their assembly processes is crucial for controllin...Excessive levels of higher alcohols have negative impacts on the quality of Baijiu.Understanding the key mi-croorganisms responsible for producing higher alcohols and their assembly processes is crucial for controlling higher alcohols in multi-species Baijiu fermentation.This study investigated the changes in volatile compounds,including higher alcohols,and microbial communities in the four fermentation cycles of Jiang-flavor Baijiu.Higher alcohols were the most abundant in the first cycle.Through metatranscriptomic and culture-dependent analysis,Saccharomyces cerevisiae and four non-Saccharomyces yeasts(Pichia kudriavzevii,Zygosaccharomyces bailii,Schizosaccharomyces pombe,and Torulaspora delbrueckii)were demonstrated to be the main contributors to higher alcohol(isobutanol,isoamylol,and 1-propanol)production,with S.cerevisiae producing the highest levels.A higher abundance of Saccharomyces resulted in the highest levels of higher alcohols in the first cycle.Moreover,our results revealed that yeast community was assembled from stochastic to deterministic processes with the increase of fermentation cycles,driven by lactic acid.These findings provide valuable insights into controlling higher alcohol production in Baijiu fermentation.展开更多
Fermented broad beans(Vicia faba L.),commonly known as meju,serve as a crucial raw material for producing Pixian Doubanjiang(DBJ),a traditional condiment in Chinese cuisine.However,there is limited information on the ...Fermented broad beans(Vicia faba L.),commonly known as meju,serve as a crucial raw material for producing Pixian Doubanjiang(DBJ),a traditional condiment in Chinese cuisine.However,there is limited information on the dynamics of fungal populations and the activity shifts of key enzymes during DBJ meju fermentation.This study aimed to elucidate the microbial composition,active genera,expressed genes and pathways during the DBJ meju fermentation.The general chemical components,free amino acids,enzymes and volatile compounds were also investigated;the correlations between active genera and physicochemical factors were analyzed,at different fermentation stages.The results demonstrated that protease was the predominant enzyme during meju fermentation.A total of 32 major volatile compounds were identified,with most alcohols and aldehydes showing a sharp increase from the early to the middle stages,followed by stabilization until the end of fermentation.Significant shifts in metatranscriptomic composition at the genus level were observed,with Aspergillus,Staphylococcus,and Tulasnella emerging as the core active genera in the process.Notably,cellulase activity was positively correlated with the presence of Tulasnella.Additionally,Aspergillus and Tulasnella were found to play a crucial role in developing the unique aroma of DBJ meju.Our findings on the succession of active genera and their correlation with physicochemical factors are expected to provide substantial evidence for potential quality control and enhancement of this renowned Chinese condiment.展开更多
Proglacial lake is an emergent source of the second most important greenhouse gas methane as the climate continues to warm,and syntrophic bacteria play a crucial role in the sediment organic matter degradation and met...Proglacial lake is an emergent source of the second most important greenhouse gas methane as the climate continues to warm,and syntrophic bacteria play a crucial role in the sediment organic matter degradation and methane production.However,our understanding of syntrophic bacteria in the proglacial lake sediments is limited.Here,we combined 16S rRNA gene amplicon sequencing,metagenomics,and metatranscriptomics to explore the diversity,function,and activity of syntrophic propionate-and butyrate-oxidizing bacteria(SPOB and SBOB)in sediments of a glacier-fed proglacial lake on the south Qinghai-Tibet Plateau.We identified a diverse array of putative SPOB and SBOB with pronounced spatial and temporal variations,many of which were central in microbial co-occurrence networks.The most abundant SBOB were Syntrophus,Syntrophorhabdus,and unclassified_Syntrophales,and the dominant SPOB included unclassified_Syntrophobacterales,Smithella,and Syntrophobacter.Lake hydrology,water depth,and associated physicochemical properties shape the spatial patterns of sediment syntrophic bacterial communities.Genome-resolved metagenomics revealed 21 and 4 genus-level novel lineages for SPOB and SBOB,respectively.Transcriptomic evidence highlighted high activity of the uncharacterized genera UBA1429(Anaerolineae)and E44-bin15(Dehalococcoidia)in propionate oxidation,and JAPLJM01(Syntrophia)as a dominant player in butyrate oxidation.This study provides the first insight into syntrophic oxidizers in proglacial lake sediments,advancing our understanding of carbon cycling and methane emission in cryosphere aquatic ecosystems.展开更多
Cyanobacteria play pivotal roles in global biogeochemical cycles and aquatic ecosystems due to their widespread distribution and significant contributions to primary production.Yet,the interactions between cyanobacter...Cyanobacteria play pivotal roles in global biogeochemical cycles and aquatic ecosystems due to their widespread distribution and significant contributions to primary production.Yet,the interactions between cyanobacteria and antibiotics remain unclear.This study revealed that Synechocystis sp.,a cyanobacterial species,removed 94.27%of 0.1 mg l^(-1) chloramphenicol(CAP)through enzyme-mediated degradation.While cytochrome P450 enzymes(CYP450s)were found unnecessary for CAP removal,a gene encoding cyanobacterial nitroreductase was significantly up-regulated(7.85-fold)under CAP exposure.The purified nitroreductase exhibited strong binding affinity to CAP(K_(d)=2.9 nM)and a Michaelis constant(K_(m))of 104.0μM.By engineering a bacterial strain with nitroreductase,94.43%of 0.1 mg l^(-1) CAP was removed within 2 h.Metagenomic and metatranscriptomic analyses showed that nitroreductase genes and transcripts are globally distributed across diverse microbial phyla.These findings uncover a novel enzyme for CAP degradation and advance sustainable biotechnologies to mitigate antibiotic pollution,addressing critical environmental challenges in aquaculture and other industries globally.展开更多
Marinisomatota(formerly recognized as Marinimicrobia,Marine Group A,and SAR406)are ubiquitous and abundant in marine environments,traditionally characterized as heterotrophic microorganisms.However,certain members of ...Marinisomatota(formerly recognized as Marinimicrobia,Marine Group A,and SAR406)are ubiquitous and abundant in marine environments,traditionally characterized as heterotrophic microorganisms.However,certain members of Mariniso-matota have demonstrated the capacity to harness light for carbon dioxide fixation and the synthesis of organic compounds,thriving in the translucent zone or transitioning between the translucent and aphotic layers.The metabolic strategies driv-ing the shift in trophic behaviors,and the factors influencing these transitions,remain largely unexplored.In this study,we investigate the metabolic strategies,ecological distribution,and dietary patterns of Marinisomatota through the analysis of metagenomic and metatranscriptomic data sourced from the global open oceans.A total of 1,588 Marinisomatota genomes were retrieved,representing one class,two orders,14 families,31 genera,and 67 species.These organisms are predomi-nantly found in low-latitude marine regions,with relative abundances ranging from 0.18 to 36.21%.Among the 14 families,S15-B10,TCS55,UBA1611,UBA2128,and UBA8226 exhibit potential for light-dependent processes associated with Crassulacean acid metabolism(M00169).Three distinct metabolic strategies were identified within Marinisomatota:MS0(photoautotrophic potential),MS1(heterotrophic with a pronounced glycolytic pathway),and MS2(heterotrophic without glycolysis).The emergence of these metabolic strategies may be a response to nutrient limitations within the ocean.This study reveals the potential for mixotrophic strategies in Marinisomatota,underscoring the critical interplay between life history traits and metabolic strategies in the evolution of novel nutritional groups.展开更多
Microbial communities drive essential bioprocesses,including the conversion of synthesis gas into biomethane,a sustainable energy source that supports circular carbon economies.In anaerobic environments,specialized co...Microbial communities drive essential bioprocesses,including the conversion of synthesis gas into biomethane,a sustainable energy source that supports circular carbon economies.In anaerobic environments,specialized consortia of bacteria and archaea facilitate syngas methanation through syntrophic interactions,where hydrogenotrophic methanogens play a central role in reducing carbon dioxide and monoxide with hydrogen.However,imbalances in gas ratios,particularly excess hydrogen,can disrupt these interactions and impair overall efficiency.Yet,the molecular mechanisms underlying microbial responses to such imbalances remain poorly understood.Here we show that hydrogen excess triggers profound metabolic and viral remodeling in a thermophilic anaerobic microbiome,leading to reduced methane yields and ecological instability.This reprogramming involves transcriptional downregulation of methanogenesis genes in the dominant archaeon Methanothermobacter thermautotrophicus,coupled with upregulation of CRISPR-Cas and restriction-modification systems that correlate with diminished activity of an associated phage,indicating activated host defenses against viral threats.Concurrently,bacterial species such as those from Tepidanaerobacteraceae enhance carbon fixation via the Wood-Ljungdahl pathway,serving as electron sinks to mitigate redox imbalance.These adaptive responses highlight the microbiome's resilience mechanisms under stress,revealing viruses as both stressors and selective forces in syntrophic systems.Such insights advance our understanding of microbiome dynamics in bioconversion processes and guide the engineering of more stable microbial consortia for optimized syngas-to-methane conversion amid variable feedstocks.展开更多
Given the role of the rumen microbiome in providing nutrients to the host ruminant,it is expected that rumen microbes contribute to inter-animal variations in feed efficiency.However,the link between microbial structu...Given the role of the rumen microbiome in providing nutrients to the host ruminant,it is expected that rumen microbes contribute to inter-animal variations in feed efficiency.However,the link between microbial structure and an“efficient”host phenotype is unclear.We hypothesized that extreme residual feed intake(RFI)phenotypes would display distinctive microbiome features regardless of the diet.In this study,we selected the 32 most extreme RFI Charolais bulls from a cohort of 100 animals fed corn-silage(CS;n=50)or grass-silage(GS;n=50)based diets.Rumen samples were obtained 3 h after feeding,at slaughter,for fermentation and metataxonomic and metatranscriptomic microbial analysis.Volatile fatty acid profiles showed no differences between diets and between extreme RFI phenotypes(P>0.05).Total bacteria and methanogen populations did not differ between extreme RFI phenotypes(P>0.05),although methanogens expressed per liquid rumen digesta weight tended to decrease in the most efficient bulls compared to the least efficient ones(P=0.10).The rumen microbial community structure differed between diets(P<0.001),and between extreme RFI phenotypes in the GS diet.In the whole dataset,we identified Succiniclasticum,Saccharofermentans,Clostridia_258483 and CAG-238 as bacteria discriminant between extreme RFI phenotypes(q<0.10).Within diets,these four genera were also discriminant in the GS diet and were all associated with the least efficient bulls.In contrast,in bulls fed the CS diet,only Saccharofermentans and Succiniclasticum were discriminant but they were positively associated with the most efficient bulls.Rumen microbial functional features did not differ between extreme RFI phenotypes but did differ between diets.In conclusion,the rumen microbiome was mainly influenced by diet,with the RFI phenotype being a marginal effector.Succiniclasticum,Saccharofermentans,Clostridia_258483,and CAG-238 were discriminant between extreme RFI phenotypes regardless of diet.However,the direction of the association with RFI was diet dependent,indicating a diet-RFI interaction and suggesting that these discriminating microbes may be suitable microbial indicator species for RFI only when considered in conjunction with the diet information.展开更多
Approaches for the cultivation-independent analysis of microbial communities are summarized as meta’omics,which predominantly includes metagenomic,-transcriptomic,-proteomic and-metabolomic studies.These have shown t...Approaches for the cultivation-independent analysis of microbial communities are summarized as meta’omics,which predominantly includes metagenomic,-transcriptomic,-proteomic and-metabolomic studies.These have shown that endophytic,root-associated and soil fungal communities are strongly shaped by associated plant species.The impact of plant identity on the composition of its litterssociated fungal community remains to be disentangled from the impact of litter chemistry.The composition of the plant community also shapes the fungal community.Most strikingly,adjacent plant species may share mycorrhizal symbionts even if the plants usually have different types of mycorrhizal fungi associated with them(ectomycorrhizal,ericoid and arbuscular mycorrhizal fungi).Environmental parameters weakly explain fungal community composition globally,and their effect is inconsistent at local and regional scales.Decrease in similarity among communities with increasing distance(i.e.distance decay)has been reported from local to global scales.This pattern is only exceptionally caused by spatial dispersal limitation of fungal propagules,but mostly due to the inability of the fungi to establish at the particular locality(i.e.environmental filtering or competitive exclusion).Fungal communities usually undergo pronounced seasonal changes and also differ between consecutive years.This indicates that development of the communities is usually not solely cyclic.Meta’omic studies challenge the classical view of plant litter decomposition.They show that mycorrhizal and(previously)endophytic fungi may be involved in plant litter decomposition and only partly support the idea of a succession from an Ascomycota to a Basidiomycota-dominated community.Furthermore,vertical separation of saprotrophic and mycorrhizal species in soil and sequential degradation from easily accessible to‘recalcitrant’plant compounds,such as lignin,can probably not be generalized.The current models of litter decomposition may therefore have to be eventually refined for certain ecosystems and environmental conditions.To gain deeper insights into fungal ecology,a meta’omic study design is outlined which focuses on environmental processes,because fungal communities are usually taxonomically diverse,but functionally redundant.This approach would initially identify dynamics of chemical shifts in the host and/or substrate by metametabolomics.Detected shifts would be subsequently linked to microbial activity by correlation with metatranscriptomic and/or metaproteomic data.A holistic trait-based approach might finally identify factors shaping taxonomic composition in communities against the dynamics of the environmental process(es)they are involved in.展开更多
文摘Metatranscriptomics—gene express profiling via DNA sequencing—is a powerful tool to identify genes that are actively expressed and might contribute to the phenotype of individual organisms or the phenome (the sum of several phenotypes) of a microbial community. Furthermore, metatranscriptome studies can result in extensive catalogues of genes that encode for enzymes of industrial relevance. In both cases, a major challenge for generating a high quality metatranscriptome is the extreme lability of RNA and its susceptibility to ubiquitous RNAses. The microbial community (the microbiome) of the cow rumen efficiently degrades lignocelullosic biomass, generates significant amounts of methane, a greenhouse gas twenty times more potent than carbon dioxide, and is of general importance for the physiological wellbeing of the host animal. Metatranscriptomes of the rumen microbiome from animals kept under different conditions and from various types of rumen-incubated biomass can be expected to provide new insights into these highly interesting phenotypes and subsequently provide the framework for an enhanced understanding of this socioeconomically important ecosystem. The ability to isolate large amounts of intact RNA will significantly facilitate accurate transcript annotation and expression profiling. Here we report a method that combines mechanical disruption with chemical homogenization of the sample material and consistently yields 1 mg of intact RNA from 1 g of rumen-incubated biofuel feedstock. The yield of total RNA obtained with our method exceeds the RNA yield achieved with previously reported isolation techniques, which renders RNA isolated with the method presented here as an ideal starting material for metatranscriptomic analyses and other molecular biology applications that require significant amounts of starting material.
基金sponsored by the Irish Research Council(IRC)as a Starting Laureate Award(Grant No.IRCLA/2017/246)IRC Postdoctoral Fellowship(Grant No.GOIPD/2023/1290).
文摘Microbial aggregates of different sizes in aerobic granular sludge(AGS)systems have been shown to exhibit distinct microbial community compositions.However,studies comparing the microbial activities of different-sized aggregates in AGS systems remain limited.In this study,genome-resolved metatranscriptomics was used to investigate microbial activity patterns within differently sized aggregates in a full-scale AGS plant.Our analysis revealed a weak correlation between the relative abundance of metagenome-assembled genomes(MAGs)and their transcriptomic activity,indicating that microbial abundance does not directly correspond to metabolic activity within the system.Flocculent sludge(FL;<0.2 mm)predominantly featured active nitrifiers and fermentative polyphosphate-accumulating organisms(PAOs)from Candidatus Phosphoribacter,while small granules(SG;0.2e1.0 mm)and large granules(LG;>1.0 mm)hosted more metabolically active PAOs affiliated with Ca.Accumulibacter.Differential gene expression analysis further supported these findings,demonstrating significantly higher expression levels of key phosphorus uptake genes associated with Ca.Accumulibacter in granular sludge(SG and LG)compared to flocculent sludge.Conversely,Ca.Phosphoribacter showed higher expression of these genes in the FL fraction.This study highlights distinct functional roles and metabolic activities of crucial microbial communities depending on aggregate size within AGS systems,offering new insights into optimizing wastewater treatment processes.
基金supported by the National Natural Science Foundation of China(Program No.31871788).
文摘In this study,the changes of flavor profile,the succession rules of active microorganisms and their correlation were analyzed during the fermentation process of industrial Sichuan radish paocai,in order to further explore the composition of ingredients that constitute the unique flavor characteristics of industrial Sichuan radish paocai,and the microorganisms and enzymes that may contribution to it.To this end,molecular sensory,high performance liquid chromatography and metatranscriptomics were employed to identify the aroma-active compounds,non-volatile compounds and active microorganisms during the 197-day fermentation process of industrial Sichuan radish paocai,respectively.Twenty aroma-active compounds were identified,of which 12 compounds had odor activity values≥1,and some off-flavor compounds were significantly lower than those of fresh radish.After 100 days of fermentation,aroma-active compounds began to accumulate extensively with the dominant active microorganisms transforming from fungi to bacteria.Among the potential formation pathways of 14 aroma-active compounds,most of which were dominated by Lactobacillus and Debaryomyces,and were contributed by other microorganisms mainly belong to Lactobacillales,Saccharomycetales and Bacillales.This study provides new insights into the flavor formation and microbial metabolic roles of industrialized paocai,as well as valuable references for screening and isolation of functional strains,expression and characterization of flavor enzymes.
文摘Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their metabolic responses to the prevailing environmental conditions.The double-RNA approach involves the simultaneous analysis of rRNA and mRNA,also termed structural and functional metatranscriptomics.By contrast,mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles,but requires either deep sequencing or effective rRNA depletion.In this review,we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional metatranscriptomics.In particular,we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields,such as rhizobiomes,antibiotic resistomes,methanomes,and viromes.Our review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.
基金supported by the National Natural Science Foundation of China(No.32170121)the Fundamental Research Funds for the Central Universities(No.3132022159).
文摘3-Methylindole(skatole)is regarded as one of the most offensive compounds in odor emission.Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic.In this study,an efficient aerobic skatole-degrading consortium was obtained.Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses.Bioinformatic analyses indicated that the skatole downstream degradation wasmainly via the catechol pathway,and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase.Genome binning and gene analyses indicated that Pseudomonas,Pseudoclavibacter,and Raineyella should cooperate with Rhodococcus for the skatole degradation process.Moreover,a pure strain Rhodococcus sp.DMU1 was successfully obtained which could utilize skatole as the sole carbon source.Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium.Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway.Collectively,our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader,and the degradation mainly proceeded via the catechol pathway.
基金supported by the National Natural Science Foundation of China(NSFC,Project N0.32372303)the Central Government Guide Local Special Fund Project for Scientific and Technological Development of Jiangxi Province(20212ZDD02008)the Vegetable Industry Technology System Post expert project of Jiangxi Province(No.JXARS-06).
文摘Laotan Suancai is a popular traditional Chinese fermented vegetable with a unique flavor.Current studies have focused on revealing the relationship between microbiota and flavor.However,the metabolism of biogenic amines(BAs),an important harmful substance,by the microbiota during Laotan Suancai fermentation remains unclear.In this study,we investigated the dynamic changes of eight BAs during the fermentation.The primary BAs,putrescine and cadaverine,reached 45.96±3.01 mg/kg and 43.10±2.37 mg/kg,respectively,at the end of fermentation.Spearman correlation analysis revealed significant correlations between BAs and 15 different species.Besides,the metabolic pathways of BAs were reconstructed via metatranscriptome and metabolome analyses.BAs.Furthermore,key microbes involved in BA metabolism in Laotan Suancai,such as Lactobacillaceae species,Picha,and Tetragenococcus halophilus,were identified.These findings improve our understanding of BA metabolism in fermented vegetables and have implications for the development of starter cultures with the ability to degrade BAs in the industrial production of Laotan Suancai.
基金supported by the National Natural Science Foundation of China(Project No.32160547)Key Research and Development Program of Jiangxi Province(20232BBF60024)+2 种基金Vegetable Industry Technology System Post Expert Project of Jiangxi Province(Project No.JXARS-06)Ten major directions of Guangdong Agricultural Science and Technology Innovation in the 14th Five-Year Plan(Project No.2023SDZG04)Key Core Agricultural Technology Tackling Project of Jiangxi Province(JXNK202303-05)。
文摘Suansun is a naturally fermented vegetable with unique flavor that depends on metabolic activities of microbiota.However,the formation mechanism of the key flavor driven by active microbiota during suansun fermentation is unclear.In this study,metatranscriptomics and metabolomics were used to analyze the key flavor profiles as well as the core functional microorganisms for flavor formation.HS-SPME-GC-MS and UPLC-Q-TOF/MS identified that organic acids,esters,alcohols,aldehydes,phenols and small peptides exert an important influence on the flavor formation of suansun.Based on the metatranscriptomic data,the metabolic network related to the formation of key flavors of suansun was reconstructed.Functional annotation further indicated that 5 genera(including Lactococcus,Enterococcus,Leuconostoc,Lactiplantibacillus and Weissella),which can actively produce enzymes that related to flavor synthesis,were the core functional microorganisms for flavor formation of suansun.These findings contributed to a better understanding of the flavor formation mechanism in suansun and other naturally-fermented foods.
基金supported by the National Key Research and Development Program of China(2018YFC2000500)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB29020000)+2 种基金the National Natural Science Foundation of China(31771481,91857101,and 81873548)the Primary Research&Development Plan of Jiangsu Province(BE2018751)the Jiangsu Provincial Medical Innovation Team(F.Zhang)。
文摘The human gut microbiome has primarily been studied through the use of fecal samples,a practice that has generated vital knowledge on the composition and functional capacities of gastrointestinal microbial communities.However,this reliance on fecal materials limits the investigation of microbial dynamics in other locations along the gastrointestinal tract(in situ),and the infrequent availability of fecal samples prevents analysis at finer temporal scales(e.g.,hours).In our study,we utilized colonic transendoscopic enteral tubing,a technology originally developed for fecal microbiota transplantation,to sample the ileocecal microbiome twice daily;metagenomic and metatranscriptomic analyses were then conducted on these samples.A total of 43 ileocecal and 28 urine and fecal samples were collected from five healthy volunteers.The ileocecal and fecal microbiomes,as profiled in the five volunteers,were found to be similar in metagenomic profiling,yet their active genes(metatranscriptome)were found to be highly distinct.Both microbiomes were perturbed after laxative exposure;over time,they exhibited reduced dissimilarity to their pre-treatment state,thereby demonstrating resilience as an innate property of the gut microbiome,although they did not fully recover within our observation time window.Sampling of the ileocecal microbiome during the day and at night revealed the existence of diurnal rhythms in a series of bacterial species and functional pathways,particularly those related to short-chain fatty acid production,such as Propionibacterium acnes and coenzyme A biosynthesis Ⅱ.Autocorrelation analysis and fluctuations decomposition further indicated the significant periodicity of the diurnal oscillations.Metabolomic profiling in the fecal and urine samples mirrored the perturbance and recovery in the gut microbiome,indicating the crucial contribution of the gut microbiome to many key metabolites involved in host health.This study provides novel insights into the human gut microbiome and its inner resilience and diurnal rhythms,as well as the potential consequences of these to the host.
基金supported by the National Natural Science Foundation of China (No.51678565)the Special Fund of China (No.AWS18J004)+1 种基金the Tianjin Natural Science Foundation (Nos.19JCYBJC_(2)3800, 19JCZDJC_(3)9800)the National Key R&D Program of China (No.2018YFD0800104)。
文摘Glycogen accumulating organisms(GAOs) are closely related to the deterioration of enhanced biological phosphorus removal systems. However, the metabolic mechanisms that drive GAOs remain unclear. Here, the two-thirds supernatant of a reactor were decanted following the anaerobic period to enrich GAOs. Long-term monitoring demonstrated that the system was stable and exhibited typical characteristics of GAOs metabolism. Acetate was completely consumed after 60 min of the anaerobic phase. The level of glycogen decreased from 0.20 to 0.14 g/gSS during the anaerobic phase, whereas the level of glycogen significantly increased to 0.21g/gSS at the end of the aerobic period. Moreover, there was almost no phosphate release and absorption in the complete periods, thus confirming the successful construction of a GAOs enrichment system. Microbial community analysis demonstrated that Ca. Contendobacter was among the core functional genera and showed the highest activity among all of the communities. Furthermore, our study is the first to identify the involvement of the ethyl-malonyl-CoA pathway in the synthesis of polyhydroxyvalerate via croR, ccr, ecm, mcd, mch and mcl genes. The Embden-Meyerhof-Parnas(EMP) pathway was preferentially used via glgP. Furthermore, the glyoxylate cycle was the main source of ATP under anaerobic conditions, whereas the tricarboxylic acid cycle provided ATP under aerobic conditions. aceA and mdh appeared to be major modulators of the glyoxylate pathway for controlling energy flow. Collectively, our findings not only revealed the crucial metabolic mechanisms in a GAOs enrichment system but also provided insights into the potential application of Ca. Contendobacter for wastewater treatment.
基金Supported by the Innovation Platform for Academicians of Hainan Province,No.YSPTZX202313Hainan Province Clinical Medical Center,No.2021818+3 种基金Hainan Provincial Health Industry Research Project,No.22A200078Hainan Provincial Postgraduate Innovation Research Project,No.Qhyb2022-133Hainan Medical University Graduate Student Innovative Research Project,No.HYYB2022A18Nanjing Medical University Fan Daiming Research Funds for Holistic Integrative Medicine,No.2020-3HIM.
文摘BACKGROUND Fecal microbiota transplantation(FMT)is a promising therapeutic approach for treating Crohn’s disease(CD).The new method of FMT,based on the automatic washing process,was named as washed microbiota transplantation(WMT).Most existing studies have focused on observing the clinical phenomena.However,the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome,metatranscriptome,and metabolome-has not yet been reported.AIM To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.METHODS We conducted a prospective,open-label,single-center clinical study.Eleven CD patients underwent WMT.Their clinical responses(defined as a decrease in their CD Activity Index score of>100 points)and their microbiome(metagenome,metatranscriptome)and metabolome profiles were evaluated three months after the procedure.RESULTS Seven of the 11 patients(63.6%)showed an optimal clinical response three months post-WMT.Gut microbiome diversity significantly increased after WMT,consistent with improved clinical symptoms.Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains,such as Faecalibac-terium prausnitzii,Roseburia intestinalis,and Escherichia coli.In addition,metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors.However,levels of vital amino acids that may be associated with disease progression(e.g.,L-glutamic acid,gamma-glutamyl-leucine,and prolyl-glutamine)were reduced after WMT.CONCLUSION WMT demonstrated therapeutic efficacy in CD treatment,likely due to the effective reconstruction of the patient’s microbiome.Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.
基金financially supported by the National Natural Science Foundation of China(42293264 and 42293262)the Postdoctoral Fellowship Program of CPSF(GZC20241196)。
文摘Phytoplankton play a vital role in nutrient biogeochemical cycling,and their elemental ratios covary with available inorganic nutrients;however,the underlying interaction patterns and mechanisms remain unclear.Here,based on large-scale and long-term field surveys together with culture experiments,we found a stoichiometric convergence over time between phytoplankton nitrogen(N)∶carbon(C)molar ratios and dissolved inorganic N∶CO_(2)molar ratios.Functional genomics evidence demonstrated that this N-C stoichiometric convergence was driven by phytoplankton community succession with its matched N and C metabolism.A theoretical framework was proposed and proved applicable for depicting this convergence.The convergence speed was faster with the greater difference between phytoplankton and water N∶C molar ratios.Moreover,replacing CO_(2)with dissolved inorganic C could alter the direction of convergence.This stoichiometric convergence characterizes the response of phytoplankton elemental ratios to inorganic nutrient dynamics and represents an evolutionary pathway for phytoplankton community assembly over time.
基金supported by grant from the Guannan County Finance Bureau,the National Natural Science Foundation of China(32302030)the China Postdoctoral Science Foundation(2023M731334).
文摘Moisture plays a pivotal role in solid-state fermentation by providing essential environmental support for microbial growth,regulating temperature and humidity,influencing metabolic efficiency,and ultimately controlling the fermentation process.This study investigated the effects of moisture on microbial community diversity,functional microorganisms,and metabolic capacity during Daqu fermentation.A room environment monitoring system was developed to collect real-time environmental parameters,revealing moisture as a key driver of microbial community succession(p=0.001).Characteristic microorganisms,including Lichtheimia,Lactiplantibacillus,Pichia,Aspergillus,and Proteus,were identified.Structural equation modeling(SEM)analysis demonstrated that microbialα-diversity exhibited a significant positive correlation with moisture(p<0.01).While increased microbialα-diversity suppressed Lichtheimia and Aspergillus(p<0.05),it significantly promoted the proliferation of Lactiplantibacillus,Pichia,and Proteus(p<0.01).Lichtheimia showed a positive correlation with saccharifying power(p<0.05)and a highly significant positive correlation with esterifying power(p<0.01).The growth of Aspergillus significantly enhanced both saccharifying and liquefying powers of Daqu(p<0.01),whereas Lactiplantibacillus,Pichia,and Proteus markedly improved fermenting power(p<0.01).Metatranscriptomic analysis revealed the expression of key functional enzymes and their microbial origins,demonstrating that Lactiplantibacillus,Pichia,and Wickerhamomyces all contributed to saccharification,liquefaction,fermentation,and esterification.These findings provide both theoretical and practical insights into the influence of moisture on microbial metabolism and the optimization of fermentation processes.
基金supported by the National Natural Science Foundation of China(NSFC)(grants 32172176,32201981)National First-class Discipline Program of Light Industry Technology and Engineering(QGJC20230301).
文摘Excessive levels of higher alcohols have negative impacts on the quality of Baijiu.Understanding the key mi-croorganisms responsible for producing higher alcohols and their assembly processes is crucial for controlling higher alcohols in multi-species Baijiu fermentation.This study investigated the changes in volatile compounds,including higher alcohols,and microbial communities in the four fermentation cycles of Jiang-flavor Baijiu.Higher alcohols were the most abundant in the first cycle.Through metatranscriptomic and culture-dependent analysis,Saccharomyces cerevisiae and four non-Saccharomyces yeasts(Pichia kudriavzevii,Zygosaccharomyces bailii,Schizosaccharomyces pombe,and Torulaspora delbrueckii)were demonstrated to be the main contributors to higher alcohol(isobutanol,isoamylol,and 1-propanol)production,with S.cerevisiae producing the highest levels.A higher abundance of Saccharomyces resulted in the highest levels of higher alcohols in the first cycle.Moreover,our results revealed that yeast community was assembled from stochastic to deterministic processes with the increase of fermentation cycles,driven by lactic acid.These findings provide valuable insights into controlling higher alcohol production in Baijiu fermentation.
基金funded by the Key R&D Projects of Chengdu Science and Technology Bureau(No.2022-YF05-00640-SN)the Science and technology project,Department of Science and Technology,Sichuan Province(No.2021ZHFP0162,2022YFS0510,22ZDYF2047 and 23ZHSF0056).
文摘Fermented broad beans(Vicia faba L.),commonly known as meju,serve as a crucial raw material for producing Pixian Doubanjiang(DBJ),a traditional condiment in Chinese cuisine.However,there is limited information on the dynamics of fungal populations and the activity shifts of key enzymes during DBJ meju fermentation.This study aimed to elucidate the microbial composition,active genera,expressed genes and pathways during the DBJ meju fermentation.The general chemical components,free amino acids,enzymes and volatile compounds were also investigated;the correlations between active genera and physicochemical factors were analyzed,at different fermentation stages.The results demonstrated that protease was the predominant enzyme during meju fermentation.A total of 32 major volatile compounds were identified,with most alcohols and aldehydes showing a sharp increase from the early to the middle stages,followed by stabilization until the end of fermentation.Significant shifts in metatranscriptomic composition at the genus level were observed,with Aspergillus,Staphylococcus,and Tulasnella emerging as the core active genera in the process.Notably,cellulase activity was positively correlated with the presence of Tulasnella.Additionally,Aspergillus and Tulasnella were found to play a crucial role in developing the unique aroma of DBJ meju.Our findings on the succession of active genera and their correlation with physicochemical factors are expected to provide substantial evidence for potential quality control and enhancement of this renowned Chinese condiment.
基金supported by the National Natural Science Foundation of China for Excellent Young Scientists Fund Program(Grant No.42222105)the National Natural Science Foundation of China General Program(Grant No.42171144),the Second Tibetan Plateau Scientific Expedition and Research Program(STEP)(Grant No.2021QZKK0100)+1 种基金the Key Research and Development Plan of Xizang Autonomous Region(Grant No.XZ202301ZY0008G)the Global Ocean Negative Carbon Emissions(Global ONCE)Program.
文摘Proglacial lake is an emergent source of the second most important greenhouse gas methane as the climate continues to warm,and syntrophic bacteria play a crucial role in the sediment organic matter degradation and methane production.However,our understanding of syntrophic bacteria in the proglacial lake sediments is limited.Here,we combined 16S rRNA gene amplicon sequencing,metagenomics,and metatranscriptomics to explore the diversity,function,and activity of syntrophic propionate-and butyrate-oxidizing bacteria(SPOB and SBOB)in sediments of a glacier-fed proglacial lake on the south Qinghai-Tibet Plateau.We identified a diverse array of putative SPOB and SBOB with pronounced spatial and temporal variations,many of which were central in microbial co-occurrence networks.The most abundant SBOB were Syntrophus,Syntrophorhabdus,and unclassified_Syntrophales,and the dominant SPOB included unclassified_Syntrophobacterales,Smithella,and Syntrophobacter.Lake hydrology,water depth,and associated physicochemical properties shape the spatial patterns of sediment syntrophic bacterial communities.Genome-resolved metagenomics revealed 21 and 4 genus-level novel lineages for SPOB and SBOB,respectively.Transcriptomic evidence highlighted high activity of the uncharacterized genera UBA1429(Anaerolineae)and E44-bin15(Dehalococcoidia)in propionate oxidation,and JAPLJM01(Syntrophia)as a dominant player in butyrate oxidation.This study provides the first insight into syntrophic oxidizers in proglacial lake sediments,advancing our understanding of carbon cycling and methane emission in cryosphere aquatic ecosystems.
基金supported by the National Natural Science Foundation of China(52470201)Anhui Provincial Key Laboratory of Environmental Pollution Control and Resource Reuse,Anhui Jianzhu University,Hefei,230601,China(no.2024EPC01).
文摘Cyanobacteria play pivotal roles in global biogeochemical cycles and aquatic ecosystems due to their widespread distribution and significant contributions to primary production.Yet,the interactions between cyanobacteria and antibiotics remain unclear.This study revealed that Synechocystis sp.,a cyanobacterial species,removed 94.27%of 0.1 mg l^(-1) chloramphenicol(CAP)through enzyme-mediated degradation.While cytochrome P450 enzymes(CYP450s)were found unnecessary for CAP removal,a gene encoding cyanobacterial nitroreductase was significantly up-regulated(7.85-fold)under CAP exposure.The purified nitroreductase exhibited strong binding affinity to CAP(K_(d)=2.9 nM)and a Michaelis constant(K_(m))of 104.0μM.By engineering a bacterial strain with nitroreductase,94.43%of 0.1 mg l^(-1) CAP was removed within 2 h.Metagenomic and metatranscriptomic analyses showed that nitroreductase genes and transcripts are globally distributed across diverse microbial phyla.These findings uncover a novel enzyme for CAP degradation and advance sustainable biotechnologies to mitigate antibiotic pollution,addressing critical environmental challenges in aquaculture and other industries globally.
基金supported by the National Natu-ral Science Foundation of China(Grant No.42030412,42206101)Sci-entific Research Foundation of Third Institute of Oceanography,MNR(No.2023003,2019021).
文摘Marinisomatota(formerly recognized as Marinimicrobia,Marine Group A,and SAR406)are ubiquitous and abundant in marine environments,traditionally characterized as heterotrophic microorganisms.However,certain members of Mariniso-matota have demonstrated the capacity to harness light for carbon dioxide fixation and the synthesis of organic compounds,thriving in the translucent zone or transitioning between the translucent and aphotic layers.The metabolic strategies driv-ing the shift in trophic behaviors,and the factors influencing these transitions,remain largely unexplored.In this study,we investigate the metabolic strategies,ecological distribution,and dietary patterns of Marinisomatota through the analysis of metagenomic and metatranscriptomic data sourced from the global open oceans.A total of 1,588 Marinisomatota genomes were retrieved,representing one class,two orders,14 families,31 genera,and 67 species.These organisms are predomi-nantly found in low-latitude marine regions,with relative abundances ranging from 0.18 to 36.21%.Among the 14 families,S15-B10,TCS55,UBA1611,UBA2128,and UBA8226 exhibit potential for light-dependent processes associated with Crassulacean acid metabolism(M00169).Three distinct metabolic strategies were identified within Marinisomatota:MS0(photoautotrophic potential),MS1(heterotrophic with a pronounced glycolytic pathway),and MS2(heterotrophic without glycolysis).The emergence of these metabolic strategies may be a response to nutrient limitations within the ocean.This study reveals the potential for mixotrophic strategies in Marinisomatota,underscoring the critical interplay between life history traits and metabolic strategies in the evolution of novel nutritional groups.
基金supported by the LIFE20 CCM/GR/001642-LIFE CO_(2)toCH_(4)of the European Union LIFE+program and the European Union's Horizon 2020 research and innovation program under grant agreement No 101084405(CRONUS).
文摘Microbial communities drive essential bioprocesses,including the conversion of synthesis gas into biomethane,a sustainable energy source that supports circular carbon economies.In anaerobic environments,specialized consortia of bacteria and archaea facilitate syngas methanation through syntrophic interactions,where hydrogenotrophic methanogens play a central role in reducing carbon dioxide and monoxide with hydrogen.However,imbalances in gas ratios,particularly excess hydrogen,can disrupt these interactions and impair overall efficiency.Yet,the molecular mechanisms underlying microbial responses to such imbalances remain poorly understood.Here we show that hydrogen excess triggers profound metabolic and viral remodeling in a thermophilic anaerobic microbiome,leading to reduced methane yields and ecological instability.This reprogramming involves transcriptional downregulation of methanogenesis genes in the dominant archaeon Methanothermobacter thermautotrophicus,coupled with upregulation of CRISPR-Cas and restriction-modification systems that correlate with diminished activity of an associated phage,indicating activated host defenses against viral threats.Concurrently,bacterial species such as those from Tepidanaerobacteraceae enhance carbon fixation via the Wood-Ljungdahl pathway,serving as electron sinks to mitigate redox imbalance.These adaptive responses highlight the microbiome's resilience mechanisms under stress,revealing viruses as both stressors and selective forces in syntrophic systems.Such insights advance our understanding of microbiome dynamics in bioconversion processes and guide the engineering of more stable microbial consortia for optimized syngas-to-methane conversion amid variable feedstocks.
基金supported by APIS-GENE(Paris,France)as part of the EffiScience project and by the European Union's Horizon 2020 research and innovation programme under grant agreements MASTER-818368 and HoloRuminant-101000213.
文摘Given the role of the rumen microbiome in providing nutrients to the host ruminant,it is expected that rumen microbes contribute to inter-animal variations in feed efficiency.However,the link between microbial structure and an“efficient”host phenotype is unclear.We hypothesized that extreme residual feed intake(RFI)phenotypes would display distinctive microbiome features regardless of the diet.In this study,we selected the 32 most extreme RFI Charolais bulls from a cohort of 100 animals fed corn-silage(CS;n=50)or grass-silage(GS;n=50)based diets.Rumen samples were obtained 3 h after feeding,at slaughter,for fermentation and metataxonomic and metatranscriptomic microbial analysis.Volatile fatty acid profiles showed no differences between diets and between extreme RFI phenotypes(P>0.05).Total bacteria and methanogen populations did not differ between extreme RFI phenotypes(P>0.05),although methanogens expressed per liquid rumen digesta weight tended to decrease in the most efficient bulls compared to the least efficient ones(P=0.10).The rumen microbial community structure differed between diets(P<0.001),and between extreme RFI phenotypes in the GS diet.In the whole dataset,we identified Succiniclasticum,Saccharofermentans,Clostridia_258483 and CAG-238 as bacteria discriminant between extreme RFI phenotypes(q<0.10).Within diets,these four genera were also discriminant in the GS diet and were all associated with the least efficient bulls.In contrast,in bulls fed the CS diet,only Saccharofermentans and Succiniclasticum were discriminant but they were positively associated with the most efficient bulls.Rumen microbial functional features did not differ between extreme RFI phenotypes but did differ between diets.In conclusion,the rumen microbiome was mainly influenced by diet,with the RFI phenotype being a marginal effector.Succiniclasticum,Saccharofermentans,Clostridia_258483,and CAG-238 were discriminant between extreme RFI phenotypes regardless of diet.However,the direction of the association with RFI was diet dependent,indicating a diet-RFI interaction and suggesting that these discriminating microbes may be suitable microbial indicator species for RFI only when considered in conjunction with the diet information.
基金funded by the Deutsche Forschungsgemeinschaft(DFG,project PE 1673/4-1).
文摘Approaches for the cultivation-independent analysis of microbial communities are summarized as meta’omics,which predominantly includes metagenomic,-transcriptomic,-proteomic and-metabolomic studies.These have shown that endophytic,root-associated and soil fungal communities are strongly shaped by associated plant species.The impact of plant identity on the composition of its litterssociated fungal community remains to be disentangled from the impact of litter chemistry.The composition of the plant community also shapes the fungal community.Most strikingly,adjacent plant species may share mycorrhizal symbionts even if the plants usually have different types of mycorrhizal fungi associated with them(ectomycorrhizal,ericoid and arbuscular mycorrhizal fungi).Environmental parameters weakly explain fungal community composition globally,and their effect is inconsistent at local and regional scales.Decrease in similarity among communities with increasing distance(i.e.distance decay)has been reported from local to global scales.This pattern is only exceptionally caused by spatial dispersal limitation of fungal propagules,but mostly due to the inability of the fungi to establish at the particular locality(i.e.environmental filtering or competitive exclusion).Fungal communities usually undergo pronounced seasonal changes and also differ between consecutive years.This indicates that development of the communities is usually not solely cyclic.Meta’omic studies challenge the classical view of plant litter decomposition.They show that mycorrhizal and(previously)endophytic fungi may be involved in plant litter decomposition and only partly support the idea of a succession from an Ascomycota to a Basidiomycota-dominated community.Furthermore,vertical separation of saprotrophic and mycorrhizal species in soil and sequential degradation from easily accessible to‘recalcitrant’plant compounds,such as lignin,can probably not be generalized.The current models of litter decomposition may therefore have to be eventually refined for certain ecosystems and environmental conditions.To gain deeper insights into fungal ecology,a meta’omic study design is outlined which focuses on environmental processes,because fungal communities are usually taxonomically diverse,but functionally redundant.This approach would initially identify dynamics of chemical shifts in the host and/or substrate by metametabolomics.Detected shifts would be subsequently linked to microbial activity by correlation with metatranscriptomic and/or metaproteomic data.A holistic trait-based approach might finally identify factors shaping taxonomic composition in communities against the dynamics of the environmental process(es)they are involved in.
