Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 3.184
Filtrar
1.
Microbiome ; 12(1): 83, 2024 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-38725008

RESUMO

BACKGROUND: Fungi and bacteria coexist in a wide variety of environments, and their interactions are now recognized as the norm in most agroecosystems. These microbial communities harbor keystone taxa, which facilitate connectivity between fungal and bacterial communities, influencing their composition and functions. The roots of most plants are associated with arbuscular mycorrhizal (AM) fungi, which develop dense networks of hyphae in the soil. The surface of these hyphae (called the hyphosphere) is the region where multiple interactions with microbial communities can occur, e.g., exchanging or responding to each other's metabolites. However, the presence and importance of keystone taxa in the AM fungal hyphosphere remain largely unknown. RESULTS: Here, we used in vitro and pot cultivation systems of AM fungi to investigate whether certain keystone bacteria were able to shape the microbial communities growing in the hyphosphere and potentially improved the fitness of the AM fungal host. Based on various AM fungi, soil leachates, and synthetic microbial communities, we found that under organic phosphorus (P) conditions, AM fungi could selectively recruit bacteria that enhanced their P nutrition and competed with less P-mobilizing bacteria. Specifically, we observed a privileged interaction between the isolate Streptomyces sp. D1 and AM fungi of the genus Rhizophagus, where (1) the carbon compounds exuded by the fungus were acquired by the bacterium which could mineralize organic P and (2) the in vitro culturable bacterial community residing on the surface of hyphae was in part regulated by Streptomyces sp. D1, primarily by inhibiting the bacteria with weak P-mineralizing ability, thereby enhancing AM fungi to acquire P. CONCLUSIONS: This work highlights the multi-functionality of the keystone bacteria Streptomyces sp. D1 in fungal-bacteria and bacterial-bacterial interactions at the hyphal surface of AM fungi. Video Abstract.


Assuntos
Hifas , Microbiota , Micorrizas , Raízes de Plantas , Microbiologia do Solo , Streptomyces , Micorrizas/fisiologia , Micorrizas/classificação , Streptomyces/classificação , Streptomyces/isolamento & purificação , Streptomyces/genética , Streptomyces/fisiologia , Hifas/crescimento & desenvolvimento , Raízes de Plantas/microbiologia , Fósforo/metabolismo , Interações Microbianas/fisiologia , Solo/química , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo
2.
Environ Microbiol Rep ; 16(3): e13276, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38733087

RESUMO

Syntrophic interactions are key in anaerobic food chains, facilitating the conversion of complex organic matter into methane. A typical example involves acetogenic bacteria converting fatty acids (e.g., butyrate and propionate), a process thermodynamically reliant on H2 consumption by microorganisms such as methanogens. While most studies focus on H2-interspecies transfer between these groups, knowledge on acetate cross-feeding in anaerobic systems is lacking. This study investigated butyrate oxidation by co-cultures of Syntrophomonas wolfei and Methanospirillum hungatei, both with and without the addition of the acetate scavenger Methanothrix soehngenii. Growth and gene expression patterns of S. wolfei and M. hungatei were followed in the two conditions. Although butyrate consumption rates remained constant, genes in the butyrate degradation pathway of S. wolfei were less expressed in the presence of M. soehngenii, including genes involved in reverse electron transport. Higher expression of a type IV-pili operon in S. wolfei hints to the potential for direct interspecies electron transfer between S. wolfei and M. soehngenii and an energetically advantageous relationship between the two microorganisms. Overall, the presence of the acetate scavenger M. soehngenii positively influenced the energy metabolism of S. wolfei and highlighted the relevance of including acetate scavengers when investigating syntrophic fatty acid degradation.


Assuntos
Methanospirillum , Methanospirillum/metabolismo , Methanospirillum/genética , Butiratos/metabolismo , Transcriptoma , Anaerobiose , Oxirredução , Acetatos/metabolismo , Interações Microbianas , Metano/metabolismo , Técnicas de Cocultura , Transporte de Elétrons
3.
ISME J ; 18(1)2024 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-38691424

RESUMO

Antibiotic persistence (heterotolerance) allows a subpopulation of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.


Assuntos
Antibacterianos , Escherichia coli , Salmonella enterica , Simbiose , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/crescimento & desenvolvimento , Antibacterianos/farmacologia , Salmonella enterica/efeitos dos fármacos , Salmonella enterica/genética , Técnicas de Cocultura , Interações Microbianas , Ampicilina/farmacologia , Farmacorresistência Bacteriana
4.
ISME J ; 18(1)2024 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-38691428

RESUMO

Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial groups in soil. This is because C and energy limitations for microbial growth are a rule rather than an exception. Here, we review the C and energy demands of bacteria and fungi-the two major kingdoms in soil-the mechanisms of their competition for these and other resources, leading to niche differentiation, and the global change impacts on this competition. The normalized microbial utilization preference showed that bacteria are 1.4-5 times more efficient in the uptake of simple organic compounds as substrates, whereas fungi are 1.1-4.1 times more effective in utilizing complex compounds. Accordingly, bacteria strongly outcompete fungi for simple substrates, while fungi take advantage of complex compounds. Bacteria also compete with fungi for the products released during the degradation of complex substrates. Based on these specifics, we differentiated spatial, temporal, and chemical niches for these two groups in soil. The competition will increase under the main five global changes including elevated CO2, N deposition, soil acidification, global warming, and drought. Elevated CO2, N deposition, and warming increase bacterial dominance, whereas soil acidification and drought increase fungal competitiveness.


Assuntos
Bactérias , Fungos , Microbiologia do Solo , Fungos/metabolismo , Fungos/crescimento & desenvolvimento , Bactérias/metabolismo , Bactérias/classificação , Bactérias/genética , Solo/química , Carbono/metabolismo , Interações Microbianas
5.
Cell Rep Methods ; 4(5): 100775, 2024 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-38744286

RESUMO

To address the limitation of overlooking crucial ecological interactions due to relying on single time point samples, we developed a computational approach that analyzes individual samples based on the interspecific microbial relationships. We verify, using both numerical simulations as well as real and shuffled microbial profiles from the human oral cavity, that the method can classify single samples based on their interspecific interactions. By analyzing the gut microbiome of people with autistic spectrum disorder, we found that our interaction-based method can improve the classification of individual subjects based on a single microbial sample. These results demonstrate that the underlying ecological interactions can be practically utilized to facilitate microbiome-based diagnosis and precision medicine.


Assuntos
Transtorno do Espectro Autista , Microbioma Gastrointestinal , Humanos , Transtorno do Espectro Autista/microbiologia , Transtorno do Espectro Autista/diagnóstico , Boca/microbiologia , Microbiota , Interações Microbianas , Simulação por Computador
6.
Sci Total Environ ; 931: 172901, 2024 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-38697549

RESUMO

High nitrate pollution in agriculture and industry poses a challenge to emerging methane oxidation coupled denitrification. In this study, an efficient nitrate removal efficiency of 100 % was achieved at an influent loading rate of 400 mg-N/L·d, accompanied by the production of short chain fatty acids (SCFAs) with a maximum value of 80.9 mg/L. Batch tests confirmed that methane was initially converted to acetate, which then served as a carbon source for denitrification. Microbial community characterization revealed the dominance of heterotrophic denitrifiers, including Simplicispira (22.8 %), Stappia (4.9 %), and the high­nitrogen-tolerant heterotrophic denitrifier Diaphorobacter (19.0 %), at the nitrate removal rate of 400 mg-N/L·d. Notably, the low abundance of methanotrophs ranging from 0.24 % to 3.75 % across all operational stages does not fully align with the abundance of pmoA genes, suggesting the presence of other functional microorganisms capable of methane oxidation and SCFAs production. These findings could facilitate highly efficient denitrification driven by methane and contributed to the development of denitrification using methane as an electron donor.


Assuntos
Desnitrificação , Ácidos Graxos Voláteis , Metano , Metano/metabolismo , Ácidos Graxos Voláteis/metabolismo , Eliminação de Resíduos Líquidos/métodos , Interações Microbianas , Nitratos/metabolismo , Reatores Biológicos/microbiologia
7.
Elife ; 122024 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-38690990

RESUMO

Caesarean section scar diverticulum (CSD) is a significant cause of infertility among women who have previously had a Caesarean section, primarily due to persistent inflammatory exudation associated with this condition. Even though abnormal bacterial composition is identified as a critical factor leading to this chronic inflammation, clinical data suggest that a long-term cure is often unattainable with antibiotic treatment alone. In our study, we employed metagenomic analysis and mass spectrometry techniques to investigate the fungal composition in CSD and its interaction with bacteria. We discovered that local fungal abnormalities in CSD can disrupt the stability of the bacterial population and the entire microbial community by altering bacterial abundance via specific metabolites. For instance, Lachnellula suecica reduces the abundance of several Lactobacillus spp., such as Lactobacillus jensenii, by diminishing the production of metabolites like Goyaglycoside A and Janthitrem E. Concurrently, Clavispora lusitaniae and Ophiocordyceps australis can synergistically impact the abundance of Lactobacillus spp. by modulating metabolite abundance. Our findings underscore that abnormal fungal composition and activity are key drivers of local bacterial dysbiosis in CSD.


Assuntos
Bactérias , Cesárea , Cicatriz , Divertículo , Feminino , Cesárea/efeitos adversos , Humanos , Divertículo/microbiologia , Divertículo/metabolismo , Bactérias/metabolismo , Bactérias/genética , Cicatriz/microbiologia , Cicatriz/metabolismo , Disbiose/microbiologia , Fungos/metabolismo , Fungos/genética , Fungos/fisiologia , Interações Microbianas , Microbiota
8.
Ecol Lett ; 27(5): e14433, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38712704

RESUMO

The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.


Assuntos
Microbiota , Benzamidas , Interações Microbianas , Phyllobacteriaceae/fisiologia , Água Subterrânea/microbiologia , Biodiversidade
9.
J Hazard Mater ; 470: 134231, 2024 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-38598881

RESUMO

Fungicides are used worldwide to improve crop yields, but they can affect non-target soil microorganisms which are essential for ecosystem functioning. Microorganisms form complex communities characterized by a myriad of interspecies interactions, yet it remains unclear to what extent non-target microorganisms are indirectly affected by fungicides through biotic interactions with sensitive taxa. To quantify such indirect effects, we fragmented a soil microbial community by filtration to alter biotic interactions and compared the effect of the fungicide hymexazol between fractions in soil microcosms. We postulated that OTUs which are indirectly affected would exhibit a different response to the fungicide across the fragmented communities. We found that hymexazol primarily affected bacterial and fungal communities through indirect effects, which were responsible for more than 75% of the shifts in relative abundance of the dominant microbial OTUs after exposure to an agronomic dose of hymexazol. However, these indirect effects decreased for the bacterial community when hymexazol doses increased. Our results also suggest that N-cycling processes such as ammonia oxidation can be impacted indirectly by fungicide application. This work sheds light on the indirect impact of fungicide exposure on soil microorganisms through biotic interactions, which underscores the need for higher-tier risk assessment. ENVIRONMENTAL IMPLICATION: In this study, we used a novel approach based on the fragmentation of the soil microbial community to determine to which extent fungicide application could indirectly affect fungi and bacteria through biotic interactions. To assess off-target effects of fungicide on soil microorganisms, we selected hymexazol, which is used worldwide to control a variety of fungal plant pathogens, and exposed arable soil to the recommended field rate, as well as to higher rates. Our findings show that at least 75% of hymexazol-impacted microbial OTUs were indirectly affected, therefore emphasizing the importance of tiered risk assessment.


Assuntos
Bactérias , Fungos , Fungicidas Industriais , Microbiologia do Solo , Fungicidas Industriais/toxicidade , Fungicidas Industriais/farmacologia , Fungos/efeitos dos fármacos , Fungos/metabolismo , Bactérias/efeitos dos fármacos , Bactérias/metabolismo , Poluentes do Solo/toxicidade , Microbiota/efeitos dos fármacos , Interações Microbianas/efeitos dos fármacos
10.
Microb Pathog ; 190: 106642, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38599551

RESUMO

The intestinal and respiratory tracts of healthy individuals serve as habitats for a diverse array of microorganisms, among which Klebsiella oxytoca holds significance as a causative agent in numerous community- and hospital-acquired infections, often manifesting in polymicrobial contexts. In specific circumstances, K. oxytoca, alongside other constituents of the gut microbiota, undergoes translocation to distinct physiological niches. In these new environments, it engages in close interactions with other microbial community members. As this interaction may progress to co-infection where the virulence of involved pathogens may be promoted and enhance disease severity, we investigated how K. oxytoca affects the adhesion of commonly co-isolated bacteria and vice versa during co-incubation of different biotic and abiotic surfaces. Co-incubation was beneficial for the adhesion of at least one of the two co-cultured strains. K. oxytoca enhanced the adhesion of other enterobacteria strains to polystyrene and adhered more efficiently to bladder or lung epithelial cell lines in the presence of most enterobacteria strains and S. aureus. This effect was accompanied by bacterial coaggregation mediated by carbohydrate-protein interactions occurring between bacteria. These interactions occur only in sessile, but not planktonic populations, and depend on the features of the surface. The data are of particular importance for the risk assessment of the urinary and respiratory tract infections caused by K. oxytoca, including those device-associated. In this paper, we present the first report on K. oxytoca ability to acquire increased adhesive capacities on epithelial cells through interactions with common causal agents of urinary and respiratory tract infections.


Assuntos
Aderência Bacteriana , Células Epiteliais , Infecções por Klebsiella , Klebsiella oxytoca , Pulmão , Bexiga Urinária , Klebsiella oxytoca/fisiologia , Humanos , Células Epiteliais/microbiologia , Pulmão/microbiologia , Infecções por Klebsiella/microbiologia , Bexiga Urinária/microbiologia , Staphylococcus aureus/fisiologia , Staphylococcus aureus/patogenicidade , Técnicas de Cocultura , Coinfecção/microbiologia , Linhagem Celular , Interações Microbianas , Infecções Oportunistas/microbiologia , Infecções Respiratórias/microbiologia , Virulência
11.
Chemosphere ; 357: 142099, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38653398

RESUMO

Vertical static composting is an efficient and convenient technology for the treatment of food waste. Exploring the impact of oxygen concentration levels on microbial community structure and functional stability is crucial for optimizing ventilation technology. This study set three experimental groups with varying ventilation intensities based on self-made alternating ventilation composting reactor (AL2: 0.2 L kg-1 DM·min-1; AL4: 0.4 L kg-1 DM·min-1; AL6: 0.6 L kg-1 DM·min-1) to explore the optimal alternating ventilation rate. The results showed that the cumulative ammonia emission of AL2 group reduced by 25.13% and 12.59% compared to the AL4 and AL6 groups. The humification degree of the product was 1.18 times and 1.25 times higher than the other two groups. AL2 increased the relative abundance of the core species Saccharomonospora, thereby strengthening microbial interaction. Low-intensity alternating ventilation increased the carbon metabolism levels, especially aerobic_chemoheterotrophy, carbohydrate and lipid metabolism. However, it simultaneously reduced nitrogen metabolism. Structural equation model analysis demonstrated that alternating low-intensity ventilation effectively regulated both microbial diversity (0.81, p < 0.001) and metabolism (0.81, p < 0.001) by shaping the composting environment. This study optimized the intensity of alternating ventilation and revealed the regulatory mechanism of community structure and metabolism. This study provides guidance for achieving efficient and low-consumption composting.


Assuntos
Carbono , Compostagem , Carbono/metabolismo , Compostagem/métodos , Alimentos , Interações Microbianas , Amônia/metabolismo , Nitrogênio/metabolismo , Substâncias Húmicas , Microbiologia do Solo , Solo/química , Eliminação de Resíduos/métodos , Perda e Desperdício de Alimentos
12.
mSystems ; 9(5): e0130523, 2024 May 16.
Artigo em Inglês | MEDLINE | ID: mdl-38682902

RESUMO

Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental understanding of how microbial interactions are driven by environmental factors, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. The effectiveness of our method was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids) but competitively grow on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions, such as asymmetry in interactions. Our approach can be extended to other ecological systems to model their environment-dependent interspecies interactions from growth kinetics.IMPORTANCEModeling environment-controlled interspecies interactions through separate identification of positive and negative influences of microbes in mixed relationships is a new capability that can significantly improve our ability to understand, predict, and engineer the complex dynamics of microbial communities. Moreover, the prediction of microbial interactions as a function of environmental variables can serve as valuable benchmark data to validate modeling and network inference tools in microbial ecology, the development of which has often been impeded due to the lack of ground truth information on interactions. While demonstrated against microbial data, the theory developed in this work is readily applicable to general community ecology to predict interactions among macroorganisms, such as plants and animals, as well as microorganisms.


Assuntos
Escherichia coli , Interações Microbianas , Interações Microbianas/fisiologia , Cinética , Escherichia coli/metabolismo , Modelos Biológicos , Meio Ambiente
13.
J Hazard Mater ; 471: 134310, 2024 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-38640677

RESUMO

Microbial interactions, particularly metabolic cross-feeding, play important roles in removing recalcitrant environmental pollutants; however, the underlying mechanisms involved in this process remain unclear. Thus, this study aimed to elucidate the mechanism by which metabolic cross-feeding occurs during synergistic dibenzofuran degradation between a highly efficient degrader, Rhodococcus sp. strain p52, and a partner incapable of utilizing dibenzofuran. A bottom-up approach combined with pairwise coculturing was used to examine metabolic cross-feeding between strain p52 and Arthrobacter sp. W06 or Achromobacter sp. D10. Pairwise coculture not only promoted bacterial pair growth but also facilitated dibenzofuran degradation. Specifically, strain p52, acting as a donor, released dibenzofuran metabolic intermediates, including salicylic acid and gentisic acid, for utilization and growth, respectively, by the partner strains W06 and D10. Both salicylic acid and gentisic acid exhibited biotoxicity, and their accumulation inhibited dibenzofuran degradation. The transcriptional activity of the genes responsible for the catabolism of dibenzofuran and its metabolic intermediates was coordinately regulated in strain p52 and its cocultivated partners, thus achieving synergistic dibenzofuran degradation. This study provides insights into microbial metabolic cross-feeding during recalcitrant environmental pollutant removal.


Assuntos
Biodegradação Ambiental , Rhodococcus , Ácido Salicílico , Rhodococcus/metabolismo , Ácido Salicílico/metabolismo , Dibenzofuranos/metabolismo , Benzofuranos/metabolismo , Gentisatos/metabolismo , Interações Microbianas
14.
Microb Ecol ; 87(1): 56, 2024 Apr 08.
Artigo em Inglês | MEDLINE | ID: mdl-38587642

RESUMO

Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.


Assuntos
Interações Microbianas , Microbiota , Humanos , Consórcios Microbianos , Técnicas de Cocultura , Redes Comunitárias
15.
FEMS Microbiol Ecol ; 100(5)2024 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-38578661

RESUMO

Cylindrospermopsis raciborskii-dominated harmful algae blooms have been reported globally in recent years. However, our understanding of the ecology of C. raciborskii in natural conditions is still poor. In this study, we collected the water samples from a C. raciborskii-blooming lake, Yilong Lake, in Yunnan province, China, and used both culture-dependent and culture-independent approaches to investigate their microbial communities and the interactions between C. raciborskii and the other bacteria. The composition and diversity of microbial communities were revealed with 16S rRNA gene high-throughput sequencing data analysis. Microbial co-occurrences analysis suggests C. raciborskii may have complex associations with other bacteria. Based on co-inoculation tests, we obtained 14 strains of bacterial strains from the water samples that exhibited either algicidal or promoting effects on a strain of C. raciborskii. Two bacterial isolates exhibited a consistent performance between co-occurrence analysis and experimental results. Effects of these bacteria-algae interspecies interactions on the bloom event are discussed. All these results may provide new insights into the C. raciborskii-dominated blooms and how its interspecies relationships with other bacteria may influence the bloom events in eutrophic waters throughout the world.


Assuntos
Bactérias , Cylindrospermopsis , Lagos , Microbiota , RNA Ribossômico 16S , Lagos/microbiologia , Cylindrospermopsis/genética , Cylindrospermopsis/crescimento & desenvolvimento , China , RNA Ribossômico 16S/genética , Bactérias/genética , Bactérias/classificação , Bactérias/isolamento & purificação , Proliferação Nociva de Algas , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , DNA Bacteriano/genética , Microbiologia da Água , Interações Microbianas
16.
Semin Cell Dev Biol ; 161-162: 22-30, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38564842

RESUMO

Modern precision sequencing techniques have established humans as a holobiont that live in symbiosis with the microbiome. Microbes play an active role throughout the life of a human ranging from metabolism and immunity to disease tolerance. Hence, it is of utmost significance to study the eukaryotic host in conjunction with the microbial antigens to obtain a complete picture of the host-microbiome crosstalk. Previous attempts at profiling host-microbiome interactions have been either superficial or been attempted to catalogue eukaryotic transcriptomic profile and microbial communities in isolation. Additionally, the nature of such immune-microbial interactions is not random but spatially organised. Hence, for a holistic clinical understanding of the interplay between hosts and microbiota, it's imperative to concurrently analyze both microbial and host genetic information, ensuring the preservation of their spatial integrity. Capturing these interactions as a snapshot in time at their site of action has the potential to transform our understanding of how microbes impact human health. In examining early-life microbial impacts, the limited presence of communities compels analysis within reduced biomass frameworks. However, with the advent of spatial transcriptomics we can address this challenge and expand our horizons of understanding these interactions in detail. In the long run, simultaneous spatial profiling of host-microbiome dialogues can have enormous clinical implications especially in gaining mechanistic insights into the disease prognosis of localised infections and inflammation. This review addresses the lacunae in host-microbiome research and highlights the importance of profiling them together to map their interactions while preserving their spatial context.


Assuntos
Microbiota , Simbiose , Humanos , Bactérias/genética , Microbiota/genética , Interações Microbianas
17.
Sheng Wu Gong Cheng Xue Bao ; 40(3): 722-738, 2024 Mar 25.
Artigo em Chinês | MEDLINE | ID: mdl-38545973

RESUMO

Synthetic microbial communities are artificial systems composed of multiple microorganisms with well-defined genetic backgrounds. They are characterized by low complexity, high controllability, and strong stability, thus suitable for industrial production, disease management, and environmental remediation. This review summarizes the design principles and construction methods of synthetic microbial communities, and highlights their application in polyhydroxyalkanoate (PHA) biosynthesis. Constructing a synthetic microbial community represents a core research direction of synthetic ecology and an emerging frontier of synthetic biology. It requires strategies to design and control microbial interactions, spatial organization, robustness maintenance, and biocontainment to obtain an efficient, stable, and controllable synthetic microbial community. In recent years, synthetic microbial communities have been widely used to synthesize high-value chemicals such as drugs, biofuels, and biomaterials. As an ideal substitute for oil-based plastics, PHA has received much attention. Enhancing the capacity and broadening the range of carbon source utilization for PHA producers have become the research priority in the application of synthetic microbial communities for PHA biosynthesis, with the aim to reduce PHA production cost.


Assuntos
Microbiota , Poli-Hidroxialcanoatos , Fermentação , Interações Microbianas
18.
mSystems ; 9(4): e0006424, 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38470039

RESUMO

During prolonged resource limitation, bacterial cells can persist in metabolically active states of non-growth. These maintenance periods, such as those experienced in stationary phase, can include upregulation of secondary metabolism and release of exometabolites into the local environment. As resource limitation is common in many environmental microbial habitats, we hypothesized that neighboring bacterial populations employ exometabolites to compete or cooperate during maintenance and that these exometabolite-facilitated interactions can drive community outcomes. Here, we evaluated the consequences of exometabolite interactions over the stationary phase among three environmental strains: Burkholderia thailandensis E264, Chromobacterium subtsugae ATCC 31532, and Pseudomonas syringae pv. tomato DC3000. We assembled them into synthetic communities that only permitted chemical interactions. We compared the responses (transcripts) and outputs (exometabolites) of each member with and without neighbors. We found that transcriptional dynamics were changed with different neighbors and that some of these changes were coordinated between members. The dominant competitor B. thailandensis consistently upregulated biosynthetic gene clusters to produce bioactive exometabolites for both exploitative and interference competition. These results demonstrate that competition strategies during maintenance can contribute to community-level outcomes. It also suggests that the traditional concept of defining competitiveness by growth outcomes may be narrow and that maintenance competition could be an additional or alternative measure. IMPORTANCE: Free-living microbial populations often persist and engage in environments that offer few or inconsistently available resources. Thus, it is important to investigate microbial interactions in this common and ecologically relevant condition of non-growth. This work investigates the consequences of resource limitation for community metabolic output and for population interactions in simple synthetic bacterial communities. Despite non-growth, we observed active, exometabolite-mediated competition among the bacterial populations. Many of these interactions and produced exometabolites were dependent on the community composition but we also observed that one dominant competitor consistently produced interfering exometabolites regardless. These results are important for predicting and understanding microbial interactions in resource-limited environments.


Assuntos
Proteínas de Bactérias , Interações Microbianas , Proteínas de Bactérias/genética , Metabolismo Secundário
19.
ISME J ; 18(1)2024 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-38537571

RESUMO

Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.


Assuntos
Microbiota , Solo/química , Microbiologia do Solo , Interações Microbianas
20.
Microbiol Spectr ; 12(5): e0228723, 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38506512

RESUMO

Understanding the interactions between microorganisms and their impact on bacterial behavior at the community level is a key research topic in microbiology. Different methods, relying on experimental or mathematical approaches based on the diverse properties of bacteria, are currently employed to study these interactions. Recently, the use of metabolic networks to understand the interactions between bacterial pairs has increased, highlighting the relevance of this approach in characterizing bacteria. In this study, we leverage the representation of bacteria through their metabolic networks to build a predictive model aimed at reducing the number of experimental assays required for designing bacterial consortia with specific behaviors. Our novel method for predicting cross-feeding or competition interactions between pairs of microorganisms utilizes metabolic network features. Machine learning classifiers are employed to determine the type of interaction from automatically reconstructed metabolic networks. Several algorithms were assessed and selected based on comprehensive testing and careful separation of manually compiled data sets obtained from literature sources. We used different classification algorithms, including K Nearest Neighbors, XGBoost, Support Vector Machine, and Random Forest, tested different parameter values, and implemented several data curation approaches to reduce the biological bias associated with our data set, ultimately achieving an accuracy of over 0.9. Our method holds substantial potential to advance the understanding of community behavior and contribute to the development of more effective approaches for consortia design.IMPORTANCEUnderstanding bacterial interactions at the community level is critical for microbiology, and leveraging metabolic networks presents an efficient and effective approach. The introduction of this novel method for predicting interactions through machine learning classifiers has the potential to advance the field by reducing the number of experimental assays required and contributing to the development of more effective bacterial consortia.


Assuntos
Algoritmos , Bactérias , Aprendizado de Máquina , Redes e Vias Metabólicas , Interações Microbianas , Bactérias/metabolismo , Bactérias/classificação , Bactérias/genética , Interações Microbianas/fisiologia , Consórcios Microbianos/fisiologia , Fenômenos Fisiológicos Bacterianos , Máquina de Vetores de Suporte , Biologia Computacional/métodos
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...