Amidst the rapid development of renewable energy,the intermittency and instability of energy supply pose severe challenges and impose higher requirements on energy storage systems.Among the various energy storage tech...Amidst the rapid development of renewable energy,the intermittency and instability of energy supply pose severe challenges and impose higher requirements on energy storage systems.Among the various energy storage technologies,the coupled approach of power-to-hydrogen(H2)and underground H2storage(UHS)offers advantages such as extended storage duration and large-scale capacity,making it highly promising for future development.However,during UHS,particularly in porous media,microbial metabolic processes such as methanogenesis,acetogenesis,and sulfate reduction may lead to H2consumption and the production of byproducts.These microbial activities can impact the efficiency and safety of UHS both positively and negatively.Therefore,this paper provides a comprehensive review of experimental,numerical,and field studies on microbial interactions in UHS within porous media,aiming to capture research progress and elucidate microbial effects.It begins by outlining the primary types of UHS and the key microbial metabolic processes involved.Subsequently,the paper introduces the experimental approaches for investigating gas-water-rock-microbe interactions and interfacial properties,the models and simulators used in numerical studies,and the procedures implemented in field trials.Furthermore,it analyzes and discusses microbial interactions and their positive and negative impacts on UHS in porous media,focusing on aspects such as H2consumption,H2flow,and storage safety.Based on these insights,recommendations for site selection,engineering operations,and on-site monitoring of UHS,as well as potential future research directions,are provided.展开更多
Ruminants utilize a wide variety of dietary substrates that are not digestible by the mammals, through microbial fermentation taking place in the rumen. Recent advanced molecular based approaches have allowed the char...Ruminants utilize a wide variety of dietary substrates that are not digestible by the mammals, through microbial fermentation taking place in the rumen. Recent advanced molecular based approaches have allowed the characterization of rumen microbiota and its compositional changes under various treatment conditions.However, the knowledge is still limited on the impacts of variations in the rumen microbiota on host biology and function. This review summarizes the information to date on host-microbial interactions in the rumen and how we can apply such information to seek the opportunities to enhance the animal performance through manipulating the rumen function.展开更多
Understanding microbial-host interactions in the oral cavity is essential for elucidating oral disease pathogenesis and its systemic implications.In vitro bacteria-host cell coculture models have enabled fundamental s...Understanding microbial-host interactions in the oral cavity is essential for elucidating oral disease pathogenesis and its systemic implications.In vitro bacteria-host cell coculture models have enabled fundamental studies to characterize bacterial infection and host responses in a reductionist yet reproducible manner.However,existing in vitro coculture models fail to establish conditions that are suitable for the growth of both mammalian cells and anaerobes,thereby hindering a comprehensive understanding of their interactions.Here,we present an asymmetric gas coculture system that simulates the oral microenvironment by maintaining distinct normoxic and anaerobic conditions for gingival epithelial cells and anaerobic bacteria,respectively.Using a key oral pathobiont,Fusobacterium nucleatum,as the primary test bed,we demonstrate that the system preserves bacterial viability and supports the integrity of telomerase-immortalized gingival keratinocytes.Compared to conventional models,this system enhanced bacterial invasion,elevated intracellular bacterial loads,and elicited more robust host pro-inflammatory responses,including increased secretion of CXCL10,IL-6,and IL-8.In addition,the model enabled precise evaluation of antibiotic efficacy against intracellular pathogens.Finally,we validate the ability of the asymmetric system to support the proliferation of a more oxygen-sensitive oral pathobiont,Porphyromonas gingivalis.These results underscore the utility of this coculture platform for studying oral microbial pathogenesis and screening therapeutics,offering a physiologically relevant approach to advance oral and systemic health research.展开更多
Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes.However,the experimental validation of the predicted interactions is challenging due to the comp...Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes.However,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria.In this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon pairs.Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days.Enriched cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were recovered.Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks.To experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise co-cultures.The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or vitamins.We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly promoted.This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks.Our work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.展开更多
Phyllosphere endophytes play a critical role in a myriad of biological functions,such as maintaining plant health and overall fitness.They play a determinative role in crop yield and quality by regulating vital proces...Phyllosphere endophytes play a critical role in a myriad of biological functions,such as maintaining plant health and overall fitness.They play a determinative role in crop yield and quality by regulating vital processes,such as leaf functionality and longevity,seed mass,apical growth,flowering,and fruit development.This study conducted a comprehensive bibliometric analysis aiming to review the prevailing research trajectories in phyllosphere endophytes and harness both primary areas of interest and emerging challenges.A total of 156 research articles on phyllosphere endophytes,published between 2002 and 2022,were retrieved from the Web of Science Core Collection(WoSCC).A systematic analysis was conducted using CiteSpace to visualize the evolution of publication frequency,the collaboration network,the co-citation network,and keywords co-occurrence.The findings indicated that initially,there were few publications on the topic of phyllosphere endophytes.However,from 2011 onwards,there was a notable increase in the number of publications on phyllosphere endophytes,gaining worldwide attention.Among authors,Arnold,A Elizabeth is widely recognized as a leading author in this research area.In terms of countries,the USA and China hold the highest rankings.As for institutional ranking,the University of Arizona is the most prevalent and leading institute in this particular subject.Collaborative efforts among the authors and institutions tend to be confined to small groups,and a large-scale collaborative network needs to be established.This study identified the influential journals,literature,and hot research topics.These findings also highlight the interconnected nature of key themes,e.g.,phyllosphere endophyte research revolves around the four pillars:diversity,fungal endophytes,growth,and endophytic fungi.This study provides an in-depth perspective on phyllosphere endophytes studies,revealing the identification of biodiversity and microbial interaction of phyllosphere endophytes as the principal research frontiers.These analytical findings not only elucidate the recent trajectory of phyllosphere endophyte research but also provide invaluable insights for similar studies and their potential applications on a global scale.展开更多
Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance th...Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival.Biofilms enable intensive inter-and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins.Here,we first discuss organization,dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome.Social interactions among bacteria,such as cooperation and competition,are discussed.We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms.Microfluidic platforms,which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with highthroughput screening and novel measurements,are also highlighted.This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.展开更多
Biological treatment processes are critical for sewage purification,wherein microbial interactions are tightly associated with treatment performance.Previous studies have focused on assessing how environmental factors...Biological treatment processes are critical for sewage purification,wherein microbial interactions are tightly associated with treatment performance.Previous studies have focused on assessing how environmental factors(such as salinity)affect the diversity and composition of the microbial community but ignore the connections among microorganisms.Here,we described the microbial interactions in response to elevated salinity in an activated sludge system by performing an association network analysis.It was found that higher salinity resulted in low microbial diversity,and small,complex,more competitive overall networks,leading to poor performance of the treatment process.Subnetworks of major phyla(Proteobacteria,Bacteroidetes,and Chloroflexi)and functional bacteria(such as AOB,NOB and denitrifiers)differed substantially under elevated salinity process.Compared with subnetworks of Nitrosomonadaceae,Nitrosomonas(AOB)made a greater contribution to nitrification under higher salinity(especially 3%)in the activated sludge system.Denitrifiers established more proportion of cooperative relationships with other bacteria to resist 3%salinity stress.Furthermore,identified keystone species playing crucial roles in maintaining process stability were dynamics and less abundant under salinity disturbance.Knowledge gleaned from this study deepened our understanding of microbial interaction in response to elevated salinity in activated sludge systems.展开更多
Anammox （ANaerobic AMMonia OXidation） is a newly discovered pathway in the nitrogen cycle. This discovery has increased our knowledge of the global nitrogen cycle and triggered intense interest for anammox-based app...Anammox （ANaerobic AMMonia OXidation） is a newly discovered pathway in the nitrogen cycle. This discovery has increased our knowledge of the global nitrogen cycle and triggered intense interest for anammox-based applications. Anammox bacteria are almost ubiquitous in the suboxic zones of almost all types of natural ecosystems and contribute significant to the global total nitrogen loss. In this paper, their ecological distributions and contributions to the nitrogen loss in marine, wetland, terrestrial ecosystems, and even extreme environments were reviewed. The unique metabolic mechanism of anammox bacteria was well described, including the particular cellular structures and genome compositions, which indicate the special evolutionary status of anammox bacteria. Finally, the ecological interactions among anammox bacteria and other organisms were discussed based on substrate availability and spatial organizations. This review attempts to summarize the fundamental understanding of anammox, provide an up-to-date summary of the knowledge of the overall anammox status, and propose future prospects for anammox. Based on novel findings, the metagenome has become a powerful tool for the genomic analysis of communities containing anammox bacteria; the metabolic diversity and biogeochemistry in the global nitrogen budget require more comprehensive studies.展开更多
An investigation was undertaken to analyse the influence of microbial inoculants on growth and enzyme activities elicited, and soil microbiome of two varieties of Chrysanthemum morifolium Ramat, which were grown under...An investigation was undertaken to analyse the influence of microbial inoculants on growth and enzyme activities elicited, and soil microbiome of two varieties of Chrysanthemum morifolium Ramat, which were grown under protected mode of cultivation. Rhizosphere soil sampling at 45 and 90 DAT(days after transplanting of cuttings) revealed up to four- to five-fold enhancement in the activity of defence-, and pathogenesisrelated, and antioxidant enzymes, relative to the uninoculated control. Plant growth and soil microbial parameters, especially soil microbial biomass carbon and potential nitrification exhibited significant increases over control. Available soil nitrogen concentrations showed 40%–44% increment in inoculated treatments. Scanning electron microscopy of the root tissues revealed biofilm-like aggregates and individual short bits of cyanobacterial filaments. Analyses of DGGE profiles of archaeal and bacterial communities did not show temporal variations(between 45 and 90 DAT). However,distinct influences on the number and abundance of phylotypes due to microbial inoculants were recorded. The inoculants — Cyanobacterial consortium(BF1- 4) and Anabaena sp.–Trichoderma sp. biofilm(An-Tr) were particularly promising in terms of the plant and soil related parameters,and remained distinct in the DGGE profiles generated. The effect of Trichoderma viride–Azotobacter biofilm on soil bacterial and archaeal communities was unique and distinct as a separate cluster. This study highlights that microbial inoculants exert positive effects, which are specific even to the rhizosphere soil microbiome of chrysanthemum varieties tested. Such inoculants can serve as soil fertility enhancing options in protected floriculture.展开更多
Microbial activity and interaction are the important driving factors in the start-up phase of food waste composting at low temperature.The aim of this study was to explore the effect of inoculating Bacillus lichenifor...Microbial activity and interaction are the important driving factors in the start-up phase of food waste composting at low temperature.The aim of this study was to explore the effect of inoculating Bacillus licheniformis on the degradation of organic components and the potential microbe-driven mechanism from the aspects of organic matter degradation,enzyme activity,microbial community interaction,and microbial metabolic function.The results showed that after inoculating B.licheniformis,temperature increased to 47.8℃ on day2,and the degradation of readily degraded carbohydrates(RDC)increased by 31.2%,and the bioheat production increased by 16.5%.There was an obvious enhancement of extracellular enzymes activities after inoculation,especially amylase activity,which increased by 7.68 times on day 4.The inoculated B.licheniformis colonized in composting as key genus in the start-up phase.Modular network analysis and Mantel test indicated that inoculation drove the cooperation between microbial network modules who were responsible for various organic components(RDC,lipid,protein,and lignocellulose)degradation in the start-up phase.Metabolic function prediction suggested that carbohydrate metabolisms including starch and sucrose metabolism,glycolysis/gluconeogenesis,pyruvate metabolism,etc.,were improved by increasing the abundance of related functional genes after inoculation.In conclusion,inoculating B.licheniformis accelerated organic degradation by driving the cooperation between microbial network modules and enhancing microbial metabolism in the start-up phase of composting.展开更多
Shanxi aged vinegar(SAV)is a famous cereal vinegar in China,which is produced through a solid-state fermentation where diverse microbes spontaneously and complex interactions occur.Here,combined with the metatranscrip...Shanxi aged vinegar(SAV)is a famous cereal vinegar in China,which is produced through a solid-state fermentation where diverse microbes spontaneously and complex interactions occur.Here,combined with the metatranscriptomics,the microbial co-occurrence network was constructed,indicating that Lactobacillus,Acetobacter and Pediococcus are the most critical genera to maintain the fermentation stability.Based on an extensive collection of 264 relevant literatures,a transport network containing 2271 reactions between microorganisms and compounds was constructed,showing that glucose(84%of all species),fructose(67%)and maltose(67%)are the most frequently utilized substrates while lactic acid(64%),acetic acid(45%)are the most frequently occurring metabolites.Specifically,the metabolic influence of species pairs was calculated using a mathematical calculation model and the metabolic influence network was constructed.The topology properties analysis found that Lactobacillus was the key role with robust metabolic control of vinegar fermentation ecosystem and acetic acid and lactic acid were the main metabolites with feedback regulation in microbial metabolism of SAV.Furthermore,systematic coordination of positive and negative impacts was proved to be inevitable to form flavor compounds and maintain a natural microbial ecosystem.This study provides a new perspective for understanding microbial interactions in fermented food.展开更多
Strawberry (Fragaria ananassa) is well known among consumers because of its attractive color, delicious taste, and nutritional benefits. It is widely grown worldwide, but its production has become a significant challe...Strawberry (Fragaria ananassa) is well known among consumers because of its attractive color, delicious taste, and nutritional benefits. It is widely grown worldwide, but its production has become a significant challenge due to changing climatic conditions that lead to abiotic stresses in plants, which results in poor root development, nutrient deficiency, and poor plant health. In this context, the major abiotic stresses are temperature fluctuations, water shortages, and high levels of soil salinity. The accumulation of salts in excessive amounts disrupts the osmotic balance and impairs physiological processes. However, drought reduces fruit size, yield, and quality. Similarly, heat and cold stresses directly affect the rate of photosynthesis. Plants respond to these changes by producing growth-promoting hormones to ensure their survival. In the context of these abiotic stresses, beneficial microbes support plant growth. Among these fungi, the most extensively studied are plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF). When applied as bioinoculants, they are associated with roots and subsequently improve soil health, fruit quality, and overall crop yield. This review highlights the impacts of abiotic stresses on strawberry roots, growth, and hormonal pathways. Moreover, it focuses on the role of beneficial soil microbes in the mitigation of these responses.展开更多
Scientists have discovered that root-dwelling bacteria directly control rice tillering-a crucial yield trait-by producing a compound that mimics plant hormones.The study,published in Cell on June 12,2025,reveals how m...Scientists have discovered that root-dwelling bacteria directly control rice tillering-a crucial yield trait-by producing a compound that mimics plant hormones.The study,published in Cell on June 12,2025,reveals how microbes partner with crops to shape agricultural productivity.展开更多
Lake mixing influences aquatic chemical properties and microbial community composition,and thus,we hypothesized that it would alter microbial community assembly and interac-tion.To clarify this issue,we explored the c...Lake mixing influences aquatic chemical properties and microbial community composition,and thus,we hypothesized that it would alter microbial community assembly and interac-tion.To clarify this issue,we explored the community assembly processes and cooccurrence networks in four seasons at two depths(epilimnion and hypolimnion)in a mesotrophic and stratified lake(Chenghai Lake),which formed stratification in the summer and turnover in the winter.During the stratification period,the epilimnion and hypolimnion went through contrary assembly processes but converged to similar assembly patterns in the mixing pe-riod.In a highly homogeneous selection environment,species with low niche breadth were filtered,resulting in decreased species richness.Water mixing in the winter homogenized the environment,resulting in a simpler microbial cooccurrence network.Interestingly,we observed a high abundance of the cyanobacterial genus Planktothrix in the winter,proba-bly due to nutrient redistribution and Planktothrix adaptivity to the winter environment in which mixing played important roles.Our study provides deeper fundamental insights into how environmental factors influence microbial community structure through community assembly processes.展开更多
Elucidating the intricate dynamics of microbial communities across soil profiles is essential for deciphering the mechanisms by which microorganisms regulate ecosystem functions.However,previous studies on soil microo...Elucidating the intricate dynamics of microbial communities across soil profiles is essential for deciphering the mechanisms by which microorganisms regulate ecosystem functions.However,previous studies on soil microorganisms have predominantly centered on abundant taxa,neglecting the significant role of rare taxa in maintaining ecosystem functions.This study comprehensively analyzed the diversity and assembly processes of both rare and abundant microbial taxa in the profiles of Udic and Ustic Isohumosols in northeast China.We also explored the relative contribution of rare and abundant microbial taxa in maintaining ecosystem multifunctionality.Results showed that rare microbial taxa exhibited a higher diversity compared to abundant taxa,and rare microbial taxa occupied more central positions within networks.Furthermore,rare taxa displayed narrower ecological niche breadths and stronger phylogenetic signals,and their community assembly was predominantly governed by deterministic processes.In contrast,stochastic processes exert more pronounced influences on the assemblage of abundant taxa.Ecosystem multifunctionality was significantly reduced in deep soil horizons relative to the surface soil horizons.This is accompanied by close cooperation of microorganisms to cope with environmental stress in deep soils.This study highlights the pivotal role of rare microbial communities in shaping multifunctionality of ecosystems across the entire soil profiles.展开更多
Advances in microbiology rely on innovations in technology. Droplet microfluidics, as a versatile and powerful technique that allows high-throughput generation and manipulation of subnanoliter volume droplets, has bec...Advances in microbiology rely on innovations in technology. Droplet microfluidics, as a versatile and powerful technique that allows high-throughput generation and manipulation of subnanoliter volume droplets, has become an indispensable tool shifting experimental paradigms in microbiology. Droplet microfluidics has opened new avenues to various microbiological research, from resolving single-cell heterogeneity to investigating spatiotemporal dynamics of microbial communities, from precise quantitation of microbiota to systematic decipherment of microbial interactions, and from isolating rare and uncultured microbes to improving genetic engineered strains. In this review, we present recent advances of droplet microfluidics in various fields of microbiology: i) microbial cultivation, ii) microorganism detection and characterization, iii) antibiotic susceptibility testing, iv) microbial interactions, v) microbial biotechnology.We also provide our perspectives on the challenges and future directions for droplet microfluidic-based microbiology research.展开更多
N fertilizer altered bacterial community compositions by changing soil nutrients.•Bacterial ammonia oxidation became predominated with the increasing N rate.•Excessive N input caused the information of a more complex ...N fertilizer altered bacterial community compositions by changing soil nutrients.•Bacterial ammonia oxidation became predominated with the increasing N rate.•Excessive N input caused the information of a more complex microbial network.•Intensified microbial competition by excessive N was due to negative link increase.Nitrogen(N)fertilization drives the structure and function of soil microbial communities,which are crucial for regulating soil biogeochemical cycling and maintaining ecosystem stability.Despite the N fertilizer effects on soil microbial composition and diversity have been widely investigated,it is generally overlooked that ecosystem processes are carried out via complex associations among microbiome members.Here,we examined the effects of five N fertilization levels(0,135,180,225,and 360 kg N ha−1)on microbial co-occurrence networks and key functional taxa such as ammonia-oxidizers in paddy soils.The results showed that N addition altered microbial community composition,which were positively related to soil total N and available phosphorus(P)contents.The abundance of ammonia-oxidizing archaea(AOA)significantly decreased after N addition,whereas ammonia-oxidizing bacteria(AOB)increased in N360 treatment.Compared with low-N group(N0 and N135),the high-N group(N225 and N360)shaped more complex microbial webs and thus improved the stability of the microbial community.Partial least squares path modeling further revealed that N fertilizer had a higher effect on microbial network complexity in the high-N group(0.83)than the low-N group(0.49).Although there were more positive links across all microbial networks,the proportion of negative links significantly increased in the high-N network,suggesting that excess N addition aggravated the competition among microbial species.Disentangling these interactions between microbial communities and N fertilization advances our understanding of biogeochemical processes in paddy soils and their effects on nutrient supply to rice production.Our findings highlighted that highly N-enriched paddy soils have more stable microbial networks and can better sustain soil ecological functions to cope with the ongoing environmental changes.展开更多
Aeromonas hydrophila,an opportunistic pathogen,often encodes Type VI Secretion System(T6SS)genes.However,the specific functions of T6SS,particularly in the context of clinical strains,remain poorly understood.In this ...Aeromonas hydrophila,an opportunistic pathogen,often encodes Type VI Secretion System(T6SS)genes.However,the specific functions of T6SS,particularly in the context of clinical strains,remain poorly understood.In this study,we characterize a multi-drug-resistant strain,AH54,which possesses a complete and functional T6SS,composed of a structural cluster and two homologous auxiliary clusters(Aux1 and Aux2).Each auxiliary cluster encodes two distinct effector proteins:a rearrangement hotspot(Rhs)protein and a proline–alanine–arginine repeat(PAAR)protein—Rhs1/PAAR1 in Aux1 and Rhs2/PAAR2 in Aux2.Our findings reveal that AH54 assembles a fully operational T6SS capable of delivering these effectors,driving inter-bacterial antagonism.Interestingly,the T6SS activity in AH54 is temperature-regulated,with enhanced secretion and antibacterial activity at lower temperatures.To protect itself from self-intoxication,AH54 produces immunity proteins(Tsi1–Tsi4)that neutralize the toxic effectors.While PAAR1 and PAAR2 are critical for Hcp secretion,immunity proteins Tsi3 and Tsi4 do not cross-protect against PAAR effectors,suggesting distinct roles for each PAAR protein in optimizing AH54's competitive fitness.In addition,using a Dictyostelium discoideum phagocytosis model,we demonstrate that Rhs2,a metal ion-dependent DNase effector,plays a crucial role in protecting AH54 from eukaryotic predation via T6SS.These findings highlight the pivotal role of T6SS in bacterial competition and pathogenesis,offering new insights into the virulence mechanisms of A.hydrophila.展开更多
Methane metabolism,driven by methanogenic and methanotrophic microorganisms,plays a pivotal role in the carbon cycle.As seawater intrusion and soil salinization rise due to global environmental shifts,understanding ho...Methane metabolism,driven by methanogenic and methanotrophic microorganisms,plays a pivotal role in the carbon cycle.As seawater intrusion and soil salinization rise due to global environmental shifts,understanding how salinity affects methane emissions,especially in deep strata,becomes imperative.Yet,insights into stratigraphic methane release under varying salinity conditions remain sparse.Here we investigate the effects of salinity on methane metabolism across terrestrial and coastal strata(15-40 m depth)through in situ and microcosm simulation studies.Coastal strata,exhibiting a salinity level five times greater than terrestrial strata,manifested a 12.05%decrease in total methane production,but a staggering 687.34%surge in methane oxidation,culminating in 146.31%diminished methane emissions.Salinity emerged as a significant factor shaping the methane-metabolizing microbial community's dynamics,impacting the methanogenic archaeal,methanotrophic archaeal,and methanotrophic bacterial communities by 16.53%,27.25%,and 22.94%,respectively.Furthermore,microbial interactions influenced strata system methane metabolism.Metabolic pathway analyses suggested Atribacteria JS1's potential role in organic matter decomposition,facilitating methane production via Methanofastidiosales.This study thus offers a comprehensive lens to comprehend stratigraphic methane emission dynamics and the overarching factors modulating them.展开更多
Changes in soil properties and microbial communities regulated rhizosphere protistan assemblages. • Bacterial community was more sensitive to soil amendments than protists and fungi. • Soil amendments trigger the role...Changes in soil properties and microbial communities regulated rhizosphere protistan assemblages. • Bacterial community was more sensitive to soil amendments than protists and fungi. • Soil amendments trigger the role of specific protistan taxa Cercozoa on microbial interactions. Understanding the responses of different rhizosphere microbial lineages to soil amendments during in situ remediation of Cd-contaminated soil is of great importance in the assessment of the restoration and crop health. Here, we evaluated the effects of lime (LM), biochar (BC), pig manure (PM), and a commercial Mg-Ca-Si conditioner (CMC) on the rice rhizosphere soil physicochemical properties and community assembly of bacteria, fungi, and protists in a six-year consecutive application of soil amendments field trial. Our results indicated that among the four amendments, the BC and CMC had the best efficiency in increasing soil pH, which were 5.2% and 16.2%, respectively. Despite the differences in soil Cd concentrations is not noticeable, all the soil amendment treatments significantly decreased the proportion of available Cd in total Cd compared to the control. Soil amendments significantly altered the diversity of bacterial community, while they had no effect on fungal and protistan communities. Linear discriminant analysis effect size (LEfSe) showed that the bacteria was more sensitive to soil amendment-induced changes. For protists, treatments with LM and BC changed the groups of protistan consumers, while treatments with PM and CMC significantly increased the relative abundances of protistan phototrophs. Co-occurrence network analysis revealed that soil amendments increased microbial network complexity and triggered the role of protists, especially for the predatory protists Cercozoa, on microbial trophic interactions. Further variation partitioning analysis revealed that edaphic properties, bacterial and fungal communities compositions together explained the 77% of the total variation in protistan community, and the stronger correlations between diversity of bacterial and protistan communities suggested that the bacteria community was a more important biotic driver of the protistan community. Overall, our findings demonstrate the distinct responses of rice rhizosphere microbial communities to soil amendment applications, highlighting the interactive associations between microbiomes, which is vital for enhancing our ability to develop effective strategies for sustainable soil management. This study enhances our understanding of the ecological roles of protists under soil amendment applications and highlights their potential contributions in bioremediation and environmental applications for Cd-contaminated soil.展开更多
基金supported by the European Union's“Horizon Europe programme”—LOC3G(Grant No.101129729)the Henan Center for Outstanding Overseas Scientists(Grant No.GZS2024001)。
文摘Amidst the rapid development of renewable energy,the intermittency and instability of energy supply pose severe challenges and impose higher requirements on energy storage systems.Among the various energy storage technologies,the coupled approach of power-to-hydrogen(H2)and underground H2storage(UHS)offers advantages such as extended storage duration and large-scale capacity,making it highly promising for future development.However,during UHS,particularly in porous media,microbial metabolic processes such as methanogenesis,acetogenesis,and sulfate reduction may lead to H2consumption and the production of byproducts.These microbial activities can impact the efficiency and safety of UHS both positively and negatively.Therefore,this paper provides a comprehensive review of experimental,numerical,and field studies on microbial interactions in UHS within porous media,aiming to capture research progress and elucidate microbial effects.It begins by outlining the primary types of UHS and the key microbial metabolic processes involved.Subsequently,the paper introduces the experimental approaches for investigating gas-water-rock-microbe interactions and interfacial properties,the models and simulators used in numerical studies,and the procedures implemented in field trials.Furthermore,it analyzes and discusses microbial interactions and their positive and negative impacts on UHS in porous media,focusing on aspects such as H2consumption,H2flow,and storage safety.Based on these insights,recommendations for site selection,engineering operations,and on-site monitoring of UHS,as well as potential future research directions,are provided.
文摘Ruminants utilize a wide variety of dietary substrates that are not digestible by the mammals, through microbial fermentation taking place in the rumen. Recent advanced molecular based approaches have allowed the characterization of rumen microbiota and its compositional changes under various treatment conditions.However, the knowledge is still limited on the impacts of variations in the rumen microbiota on host biology and function. This review summarizes the information to date on host-microbial interactions in the rumen and how we can apply such information to seek the opportunities to enhance the animal performance through manipulating the rumen function.
基金supported by National Science Foundation CAREER (2238972)National Institute of Dental and Craniofacial Research awards (R03DE031329 and R01DE030943)The Translational Tissue Modeling Laboratory is supported by the University of Michigan (Center for Gastrointestinal Research,Office of the Dean, Comprehensive Cancer Center, and the Departments of Pathology, Pharmacology, and Internal Medicine) with additional funding from the Endowment for Basic Sciences
文摘Understanding microbial-host interactions in the oral cavity is essential for elucidating oral disease pathogenesis and its systemic implications.In vitro bacteria-host cell coculture models have enabled fundamental studies to characterize bacterial infection and host responses in a reductionist yet reproducible manner.However,existing in vitro coculture models fail to establish conditions that are suitable for the growth of both mammalian cells and anaerobes,thereby hindering a comprehensive understanding of their interactions.Here,we present an asymmetric gas coculture system that simulates the oral microenvironment by maintaining distinct normoxic and anaerobic conditions for gingival epithelial cells and anaerobic bacteria,respectively.Using a key oral pathobiont,Fusobacterium nucleatum,as the primary test bed,we demonstrate that the system preserves bacterial viability and supports the integrity of telomerase-immortalized gingival keratinocytes.Compared to conventional models,this system enhanced bacterial invasion,elevated intracellular bacterial loads,and elicited more robust host pro-inflammatory responses,including increased secretion of CXCL10,IL-6,and IL-8.In addition,the model enabled precise evaluation of antibiotic efficacy against intracellular pathogens.Finally,we validate the ability of the asymmetric system to support the proliferation of a more oxygen-sensitive oral pathobiont,Porphyromonas gingivalis.These results underscore the utility of this coculture platform for studying oral microbial pathogenesis and screening therapeutics,offering a physiologically relevant approach to advance oral and systemic health research.
基金supported by the National Key Research and Development Program of China(2021YFA0717002)Taishan Young Scholars(tsqn202306029).
文摘Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes.However,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria.In this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon pairs.Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days.Enriched cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were recovered.Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks.To experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise co-cultures.The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or vitamins.We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly promoted.This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks.Our work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.
基金supported by the Research Foundation of Fujian Provincial Tobacco Monopoly Bureau(2021350000240082,2019350000240009)the Science and Technology Innovation Foundation of FAFU(CXZX2020076A)the Open Research Foundation of International Magnesium Institute(IMI2018-09).
文摘Phyllosphere endophytes play a critical role in a myriad of biological functions,such as maintaining plant health and overall fitness.They play a determinative role in crop yield and quality by regulating vital processes,such as leaf functionality and longevity,seed mass,apical growth,flowering,and fruit development.This study conducted a comprehensive bibliometric analysis aiming to review the prevailing research trajectories in phyllosphere endophytes and harness both primary areas of interest and emerging challenges.A total of 156 research articles on phyllosphere endophytes,published between 2002 and 2022,were retrieved from the Web of Science Core Collection(WoSCC).A systematic analysis was conducted using CiteSpace to visualize the evolution of publication frequency,the collaboration network,the co-citation network,and keywords co-occurrence.The findings indicated that initially,there were few publications on the topic of phyllosphere endophytes.However,from 2011 onwards,there was a notable increase in the number of publications on phyllosphere endophytes,gaining worldwide attention.Among authors,Arnold,A Elizabeth is widely recognized as a leading author in this research area.In terms of countries,the USA and China hold the highest rankings.As for institutional ranking,the University of Arizona is the most prevalent and leading institute in this particular subject.Collaborative efforts among the authors and institutions tend to be confined to small groups,and a large-scale collaborative network needs to be established.This study identified the influential journals,literature,and hot research topics.These findings also highlight the interconnected nature of key themes,e.g.,phyllosphere endophyte research revolves around the four pillars:diversity,fungal endophytes,growth,and endophytic fungi.This study provides an in-depth perspective on phyllosphere endophytes studies,revealing the identification of biodiversity and microbial interaction of phyllosphere endophytes as the principal research frontiers.These analytical findings not only elucidate the recent trajectory of phyllosphere endophyte research but also provide invaluable insights for similar studies and their potential applications on a global scale.
基金supported by the National Natural Science Foundation of China(41877029)the National Basic Research Program of China(2016YFD0800206)the Fundamental Research Funds for the Central Universities(2662017JC008).
文摘Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival.Biofilms enable intensive inter-and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins.Here,we first discuss organization,dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome.Social interactions among bacteria,such as cooperation and competition,are discussed.We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms.Microfluidic platforms,which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with highthroughput screening and novel measurements,are also highlighted.This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.
基金supported by the Open Research Fund Program of State Environmental Protection Key Laboratory of Food Chain Pollution Control(China)(FC2022YB08)the Fundamental Research Funds for the Central Universities(China)(JD2227).
文摘Biological treatment processes are critical for sewage purification,wherein microbial interactions are tightly associated with treatment performance.Previous studies have focused on assessing how environmental factors(such as salinity)affect the diversity and composition of the microbial community but ignore the connections among microorganisms.Here,we described the microbial interactions in response to elevated salinity in an activated sludge system by performing an association network analysis.It was found that higher salinity resulted in low microbial diversity,and small,complex,more competitive overall networks,leading to poor performance of the treatment process.Subnetworks of major phyla(Proteobacteria,Bacteroidetes,and Chloroflexi)and functional bacteria(such as AOB,NOB and denitrifiers)differed substantially under elevated salinity process.Compared with subnetworks of Nitrosomonadaceae,Nitrosomonas(AOB)made a greater contribution to nitrification under higher salinity(especially 3%)in the activated sludge system.Denitrifiers established more proportion of cooperative relationships with other bacteria to resist 3%salinity stress.Furthermore,identified keystone species playing crucial roles in maintaining process stability were dynamics and less abundant under salinity disturbance.Knowledge gleaned from this study deepened our understanding of microbial interaction in response to elevated salinity in activated sludge systems.
文摘Anammox （ANaerobic AMMonia OXidation） is a newly discovered pathway in the nitrogen cycle. This discovery has increased our knowledge of the global nitrogen cycle and triggered intense interest for anammox-based applications. Anammox bacteria are almost ubiquitous in the suboxic zones of almost all types of natural ecosystems and contribute significant to the global total nitrogen loss. In this paper, their ecological distributions and contributions to the nitrogen loss in marine, wetland, terrestrial ecosystems, and even extreme environments were reviewed. The unique metabolic mechanism of anammox bacteria was well described, including the particular cellular structures and genome compositions, which indicate the special evolutionary status of anammox bacteria. Finally, the ecological interactions among anammox bacteria and other organisms were discussed based on substrate availability and spatial organizations. This review attempts to summarize the fundamental understanding of anammox, provide an up-to-date summary of the knowledge of the overall anammox status, and propose future prospects for anammox. Based on novel findings, the metagenome has become a powerful tool for the genomic analysis of communities containing anammox bacteria; the metabolic diversity and biogeochemistry in the global nitrogen budget require more comprehensive studies.
基金funded by the AMAAS Network Project on Microorganisms(IARI Code:12/122)granted by ICAR to RP and the SERB project(SR/S0/PS/164/2010)DST,Government of India granted to BR
文摘An investigation was undertaken to analyse the influence of microbial inoculants on growth and enzyme activities elicited, and soil microbiome of two varieties of Chrysanthemum morifolium Ramat, which were grown under protected mode of cultivation. Rhizosphere soil sampling at 45 and 90 DAT(days after transplanting of cuttings) revealed up to four- to five-fold enhancement in the activity of defence-, and pathogenesisrelated, and antioxidant enzymes, relative to the uninoculated control. Plant growth and soil microbial parameters, especially soil microbial biomass carbon and potential nitrification exhibited significant increases over control. Available soil nitrogen concentrations showed 40%–44% increment in inoculated treatments. Scanning electron microscopy of the root tissues revealed biofilm-like aggregates and individual short bits of cyanobacterial filaments. Analyses of DGGE profiles of archaeal and bacterial communities did not show temporal variations(between 45 and 90 DAT). However,distinct influences on the number and abundance of phylotypes due to microbial inoculants were recorded. The inoculants — Cyanobacterial consortium(BF1- 4) and Anabaena sp.–Trichoderma sp. biofilm(An-Tr) were particularly promising in terms of the plant and soil related parameters,and remained distinct in the DGGE profiles generated. The effect of Trichoderma viride–Azotobacter biofilm on soil bacterial and archaeal communities was unique and distinct as a separate cluster. This study highlights that microbial inoculants exert positive effects, which are specific even to the rhizosphere soil microbiome of chrysanthemum varieties tested. Such inoculants can serve as soil fertility enhancing options in protected floriculture.
基金supported by the Open Research Fund Program of State Environmental Protection Key Laboratory of Food Chain Pollution Control(No.FC2022YB01)the National Natural Science Foundation of China(No.32071552)+1 种基金the Independent Research Project of Science and Technology Innovation Base in Tibet Autonomous Region(No.XZ2022JR0007G)China Agricultural University-Dabeinong Group Professional degree graduate joint training reform project(No.CAUDBN PDG-JTRP).
文摘Microbial activity and interaction are the important driving factors in the start-up phase of food waste composting at low temperature.The aim of this study was to explore the effect of inoculating Bacillus licheniformis on the degradation of organic components and the potential microbe-driven mechanism from the aspects of organic matter degradation,enzyme activity,microbial community interaction,and microbial metabolic function.The results showed that after inoculating B.licheniformis,temperature increased to 47.8℃ on day2,and the degradation of readily degraded carbohydrates(RDC)increased by 31.2%,and the bioheat production increased by 16.5%.There was an obvious enhancement of extracellular enzymes activities after inoculation,especially amylase activity,which increased by 7.68 times on day 4.The inoculated B.licheniformis colonized in composting as key genus in the start-up phase.Modular network analysis and Mantel test indicated that inoculation drove the cooperation between microbial network modules who were responsible for various organic components(RDC,lipid,protein,and lignocellulose)degradation in the start-up phase.Metabolic function prediction suggested that carbohydrate metabolisms including starch and sucrose metabolism,glycolysis/gluconeogenesis,pyruvate metabolism,etc.,were improved by increasing the abundance of related functional genes after inoculation.In conclusion,inoculating B.licheniformis accelerated organic degradation by driving the cooperation between microbial network modules and enhancing microbial metabolism in the start-up phase of composting.
基金supported by the National Natural Science Foundation of China(32472324)Innovation Fund of Haihe Laboratory of Synthetic Biology(22HHSWSS00013)+1 种基金Key Research and Development Projects of Shanxi Province(202202140601018)Shanxi Provincial Department of Science and Technology(202204010931002)。
文摘Shanxi aged vinegar(SAV)is a famous cereal vinegar in China,which is produced through a solid-state fermentation where diverse microbes spontaneously and complex interactions occur.Here,combined with the metatranscriptomics,the microbial co-occurrence network was constructed,indicating that Lactobacillus,Acetobacter and Pediococcus are the most critical genera to maintain the fermentation stability.Based on an extensive collection of 264 relevant literatures,a transport network containing 2271 reactions between microorganisms and compounds was constructed,showing that glucose(84%of all species),fructose(67%)and maltose(67%)are the most frequently utilized substrates while lactic acid(64%),acetic acid(45%)are the most frequently occurring metabolites.Specifically,the metabolic influence of species pairs was calculated using a mathematical calculation model and the metabolic influence network was constructed.The topology properties analysis found that Lactobacillus was the key role with robust metabolic control of vinegar fermentation ecosystem and acetic acid and lactic acid were the main metabolites with feedback regulation in microbial metabolism of SAV.Furthermore,systematic coordination of positive and negative impacts was proved to be inevitable to form flavor compounds and maintain a natural microbial ecosystem.This study provides a new perspective for understanding microbial interactions in fermented food.
文摘Strawberry (Fragaria ananassa) is well known among consumers because of its attractive color, delicious taste, and nutritional benefits. It is widely grown worldwide, but its production has become a significant challenge due to changing climatic conditions that lead to abiotic stresses in plants, which results in poor root development, nutrient deficiency, and poor plant health. In this context, the major abiotic stresses are temperature fluctuations, water shortages, and high levels of soil salinity. The accumulation of salts in excessive amounts disrupts the osmotic balance and impairs physiological processes. However, drought reduces fruit size, yield, and quality. Similarly, heat and cold stresses directly affect the rate of photosynthesis. Plants respond to these changes by producing growth-promoting hormones to ensure their survival. In the context of these abiotic stresses, beneficial microbes support plant growth. Among these fungi, the most extensively studied are plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF). When applied as bioinoculants, they are associated with roots and subsequently improve soil health, fruit quality, and overall crop yield. This review highlights the impacts of abiotic stresses on strawberry roots, growth, and hormonal pathways. Moreover, it focuses on the role of beneficial soil microbes in the mitigation of these responses.
文摘Scientists have discovered that root-dwelling bacteria directly control rice tillering-a crucial yield trait-by producing a compound that mimics plant hormones.The study,published in Cell on June 12,2025,reveals how microbes partner with crops to shape agricultural productivity.
基金This work was supported by the National Natural Science Foundation of China(No.51578537)Chinese Academy of Sciences(No.QYZDY-SSW-DQC004)。
文摘Lake mixing influences aquatic chemical properties and microbial community composition,and thus,we hypothesized that it would alter microbial community assembly and interac-tion.To clarify this issue,we explored the community assembly processes and cooccurrence networks in four seasons at two depths(epilimnion and hypolimnion)in a mesotrophic and stratified lake(Chenghai Lake),which formed stratification in the summer and turnover in the winter.During the stratification period,the epilimnion and hypolimnion went through contrary assembly processes but converged to similar assembly patterns in the mixing pe-riod.In a highly homogeneous selection environment,species with low niche breadth were filtered,resulting in decreased species richness.Water mixing in the winter homogenized the environment,resulting in a simpler microbial cooccurrence network.Interestingly,we observed a high abundance of the cyanobacterial genus Planktothrix in the winter,proba-bly due to nutrient redistribution and Planktothrix adaptivity to the winter environment in which mixing played important roles.Our study provides deeper fundamental insights into how environmental factors influence microbial community structure through community assembly processes.
基金supported by the National Natural Science Foundation of China(Grant No.41977202)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDA28020201)the Heilongjiang Provincial Natural Science Foundation of China(Grant No.ZD2022D001).
文摘Elucidating the intricate dynamics of microbial communities across soil profiles is essential for deciphering the mechanisms by which microorganisms regulate ecosystem functions.However,previous studies on soil microorganisms have predominantly centered on abundant taxa,neglecting the significant role of rare taxa in maintaining ecosystem functions.This study comprehensively analyzed the diversity and assembly processes of both rare and abundant microbial taxa in the profiles of Udic and Ustic Isohumosols in northeast China.We also explored the relative contribution of rare and abundant microbial taxa in maintaining ecosystem multifunctionality.Results showed that rare microbial taxa exhibited a higher diversity compared to abundant taxa,and rare microbial taxa occupied more central positions within networks.Furthermore,rare taxa displayed narrower ecological niche breadths and stronger phylogenetic signals,and their community assembly was predominantly governed by deterministic processes.In contrast,stochastic processes exert more pronounced influences on the assemblage of abundant taxa.Ecosystem multifunctionality was significantly reduced in deep soil horizons relative to the surface soil horizons.This is accompanied by close cooperation of microorganisms to cope with environmental stress in deep soils.This study highlights the pivotal role of rare microbial communities in shaping multifunctionality of ecosystems across the entire soil profiles.
基金supported by National Natural Science Foundation of China (Nos. 82173774, 31925037, 22104041)the Fundamental Research Funds for the Central Universities (Nos 2662021DKQD001, 2662021JC001)the Cheeloo Scholar Program of Shandong University (to W. Liu)。
文摘Advances in microbiology rely on innovations in technology. Droplet microfluidics, as a versatile and powerful technique that allows high-throughput generation and manipulation of subnanoliter volume droplets, has become an indispensable tool shifting experimental paradigms in microbiology. Droplet microfluidics has opened new avenues to various microbiological research, from resolving single-cell heterogeneity to investigating spatiotemporal dynamics of microbial communities, from precise quantitation of microbiota to systematic decipherment of microbial interactions, and from isolating rare and uncultured microbes to improving genetic engineered strains. In this review, we present recent advances of droplet microfluidics in various fields of microbiology: i) microbial cultivation, ii) microorganism detection and characterization, iii) antibiotic susceptibility testing, iv) microbial interactions, v) microbial biotechnology.We also provide our perspectives on the challenges and future directions for droplet microfluidic-based microbiology research.
基金financially supported by the Joint Funds of the National Natural Science of China(U21A20237).
文摘N fertilizer altered bacterial community compositions by changing soil nutrients.•Bacterial ammonia oxidation became predominated with the increasing N rate.•Excessive N input caused the information of a more complex microbial network.•Intensified microbial competition by excessive N was due to negative link increase.Nitrogen(N)fertilization drives the structure and function of soil microbial communities,which are crucial for regulating soil biogeochemical cycling and maintaining ecosystem stability.Despite the N fertilizer effects on soil microbial composition and diversity have been widely investigated,it is generally overlooked that ecosystem processes are carried out via complex associations among microbiome members.Here,we examined the effects of five N fertilization levels(0,135,180,225,and 360 kg N ha−1)on microbial co-occurrence networks and key functional taxa such as ammonia-oxidizers in paddy soils.The results showed that N addition altered microbial community composition,which were positively related to soil total N and available phosphorus(P)contents.The abundance of ammonia-oxidizing archaea(AOA)significantly decreased after N addition,whereas ammonia-oxidizing bacteria(AOB)increased in N360 treatment.Compared with low-N group(N0 and N135),the high-N group(N225 and N360)shaped more complex microbial webs and thus improved the stability of the microbial community.Partial least squares path modeling further revealed that N fertilizer had a higher effect on microbial network complexity in the high-N group(0.83)than the low-N group(0.49).Although there were more positive links across all microbial networks,the proportion of negative links significantly increased in the high-N network,suggesting that excess N addition aggravated the competition among microbial species.Disentangling these interactions between microbial communities and N fertilization advances our understanding of biogeochemical processes in paddy soils and their effects on nutrient supply to rice production.Our findings highlighted that highly N-enriched paddy soils have more stable microbial networks and can better sustain soil ecological functions to cope with the ongoing environmental changes.
基金supported by the National Natural Science Foundation of China under Grants(32270061 and 32100019)Shenzhen Science and Technology Program under Grant(KQTD20200909113758004).
文摘Aeromonas hydrophila,an opportunistic pathogen,often encodes Type VI Secretion System(T6SS)genes.However,the specific functions of T6SS,particularly in the context of clinical strains,remain poorly understood.In this study,we characterize a multi-drug-resistant strain,AH54,which possesses a complete and functional T6SS,composed of a structural cluster and two homologous auxiliary clusters(Aux1 and Aux2).Each auxiliary cluster encodes two distinct effector proteins:a rearrangement hotspot(Rhs)protein and a proline–alanine–arginine repeat(PAAR)protein—Rhs1/PAAR1 in Aux1 and Rhs2/PAAR2 in Aux2.Our findings reveal that AH54 assembles a fully operational T6SS capable of delivering these effectors,driving inter-bacterial antagonism.Interestingly,the T6SS activity in AH54 is temperature-regulated,with enhanced secretion and antibacterial activity at lower temperatures.To protect itself from self-intoxication,AH54 produces immunity proteins(Tsi1–Tsi4)that neutralize the toxic effectors.While PAAR1 and PAAR2 are critical for Hcp secretion,immunity proteins Tsi3 and Tsi4 do not cross-protect against PAAR effectors,suggesting distinct roles for each PAAR protein in optimizing AH54's competitive fitness.In addition,using a Dictyostelium discoideum phagocytosis model,we demonstrate that Rhs2,a metal ion-dependent DNase effector,plays a crucial role in protecting AH54 from eukaryotic predation via T6SS.These findings highlight the pivotal role of T6SS in bacterial competition and pathogenesis,offering new insights into the virulence mechanisms of A.hydrophila.
基金supported by the Key R&D Program of Zhejiang(No.2022C03010).
文摘Methane metabolism,driven by methanogenic and methanotrophic microorganisms,plays a pivotal role in the carbon cycle.As seawater intrusion and soil salinization rise due to global environmental shifts,understanding how salinity affects methane emissions,especially in deep strata,becomes imperative.Yet,insights into stratigraphic methane release under varying salinity conditions remain sparse.Here we investigate the effects of salinity on methane metabolism across terrestrial and coastal strata(15-40 m depth)through in situ and microcosm simulation studies.Coastal strata,exhibiting a salinity level five times greater than terrestrial strata,manifested a 12.05%decrease in total methane production,but a staggering 687.34%surge in methane oxidation,culminating in 146.31%diminished methane emissions.Salinity emerged as a significant factor shaping the methane-metabolizing microbial community's dynamics,impacting the methanogenic archaeal,methanotrophic archaeal,and methanotrophic bacterial communities by 16.53%,27.25%,and 22.94%,respectively.Furthermore,microbial interactions influenced strata system methane metabolism.Metabolic pathway analyses suggested Atribacteria JS1's potential role in organic matter decomposition,facilitating methane production via Methanofastidiosales.This study thus offers a comprehensive lens to comprehend stratigraphic methane emission dynamics and the overarching factors modulating them.
基金supported by the National Natural Science Foundation of China (42 177 007)China Agriculture Research System of MOF and MARA (CARS-04)+1 种基金the Natural Science Foundation of Zhejiang Province (LGN22D010004)Ningbo Natural Science Foundation (No.2022S111).
文摘Changes in soil properties and microbial communities regulated rhizosphere protistan assemblages. • Bacterial community was more sensitive to soil amendments than protists and fungi. • Soil amendments trigger the role of specific protistan taxa Cercozoa on microbial interactions. Understanding the responses of different rhizosphere microbial lineages to soil amendments during in situ remediation of Cd-contaminated soil is of great importance in the assessment of the restoration and crop health. Here, we evaluated the effects of lime (LM), biochar (BC), pig manure (PM), and a commercial Mg-Ca-Si conditioner (CMC) on the rice rhizosphere soil physicochemical properties and community assembly of bacteria, fungi, and protists in a six-year consecutive application of soil amendments field trial. Our results indicated that among the four amendments, the BC and CMC had the best efficiency in increasing soil pH, which were 5.2% and 16.2%, respectively. Despite the differences in soil Cd concentrations is not noticeable, all the soil amendment treatments significantly decreased the proportion of available Cd in total Cd compared to the control. Soil amendments significantly altered the diversity of bacterial community, while they had no effect on fungal and protistan communities. Linear discriminant analysis effect size (LEfSe) showed that the bacteria was more sensitive to soil amendment-induced changes. For protists, treatments with LM and BC changed the groups of protistan consumers, while treatments with PM and CMC significantly increased the relative abundances of protistan phototrophs. Co-occurrence network analysis revealed that soil amendments increased microbial network complexity and triggered the role of protists, especially for the predatory protists Cercozoa, on microbial trophic interactions. Further variation partitioning analysis revealed that edaphic properties, bacterial and fungal communities compositions together explained the 77% of the total variation in protistan community, and the stronger correlations between diversity of bacterial and protistan communities suggested that the bacteria community was a more important biotic driver of the protistan community. Overall, our findings demonstrate the distinct responses of rice rhizosphere microbial communities to soil amendment applications, highlighting the interactive associations between microbiomes, which is vital for enhancing our ability to develop effective strategies for sustainable soil management. This study enhances our understanding of the ecological roles of protists under soil amendment applications and highlights their potential contributions in bioremediation and environmental applications for Cd-contaminated soil.
