Hasil untuk "Microbial ecology"

D. Ning, M. Yuan, Linwei Wu et al.

Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93–0.99), precision (0.80–0.94), sensitivity (0.82–0.94), and specificity (0.95–0.98) on simulated communities, which are 10–160% higher than those from the entire community-based approach. Application of iCAMP to grassland microbial communities in response to experimental warming reveals dominant roles of homogeneous selection (38%) and ‘drift’ (59%). Interestingly, warming decreases ‘drift’ over time, and enhances homogeneous selection which is primarily imposed on Bacillales. In addition, homogeneous selection has higher correlations with drought and plant productivity under warming than control. iCAMP provides an effective and robust tool to quantify microbial assembly processes, and should also be useful for plant and animal ecology. Studies of microbial community assembly mechanisms typically use metrics for turnover within the whole community. Here, the authors develop an alternative approach based on turnover within lineages and dissect mechanistic change in grassland bacterial assembly under experimental warming.

L. Amaral-Zettler, E. Zettler, T. Mincer

Kateryna Zhalnina, Katherine B. Louie, Z. Hao et al.

N. Salzman, Kuiechun Hung, Dipica Haribhai et al.

Antimicrobial peptides are important effectors of innate immunity throughout the plant and animal kingdoms. In the mammalian small intestine, Paneth cell α-defensins are antimicrobial peptides that contribute to host defense against enteric pathogens. To determine if α-defensins also govern intestinal microbial ecology, we analyzed the intestinal microbiota of mice expressing a human α-defensin gene (DEFA5) and in mice lacking an enzyme required for the processing of mouse α-defensins. In these complementary models, we detected significant α-defensin-dependent changes in microbiota composition, but not in total bacterial numbers. Furthermore, DEFA5-expressing mice had striking losses of segmented filamentous bacteria and fewer interleukin 17 (IL-17)-producing lamina propria T cells. Our data ascribe a new homeostatic role to α-defensins in regulating the makeup of the commensal microbiota.

R. Mackie, A. Sghir, H. Gaskins

S. Radajewski, P. Ineson, N. Parekh et al.

F. Bastida, D. Eldridge, C. García et al.

The relationship between biodiversity and biomass has been a long standing debate in ecology. Soil biodiversity and biomass are essential drivers of ecosystem functions. However, unlike plant communities, little is known about how the diversity and biomass of soil microbial communities are interlinked across globally distributed biomes, and how variations in this relationship influence ecosystem function. To fill this knowledge gap, we conducted a field survey across global biomes, with contrasting vegetation and climate types. We show that soil carbon (C) content is associated to the microbial diversity–biomass relationship and ratio in soils across global biomes. This ratio provides an integrative index to identify those locations on Earth wherein diversity is much higher compared with biomass and vice versa. The soil microbial diversity-to-biomass ratio peaks in arid environments with low C content, and is very low in C-rich cold environments. Our study further advances that the reductions in soil C content associated with land use intensification and climate change could cause dramatic shifts in the microbial diversity-biomass ratio, with potential consequences for broad soil processes.

M. O’Callaghan, R. Ballard, D. Wright

The burgeoning global market for soil microbial inoculants for use in agriculture is being driven by pressure to increase sustainable crop production by managing pests and diseases without environmental impacts. Microbial inoculants, based predominantly on bacteria and fungi, are applied to soil as alternatives to conventional inorganic fertilizers (biofertilizers) or to carry out specific functions including biocontrol of pests and diseases (biopesticides), or for bioremediation and enhancement of soil characteristics. While some soil inoculants such as rhizobia have a long and successful history of use, others have performed inconsistently in the field and failed to live up to their promise suggested by laboratory testing. A more precise understanding of the ecology and modes of action of inoculant strains is key to optimizing their efficacy and guiding their targeted use to situations where they address key limitations to crop production. This will require greater collaboration between science disciplines, including microbiology, plant and soil science, molecular biology and agronomy. Inoculants must be produced and formulated to ensure their effective establishment in the soil and practicality of implementation alongside existing cropping practices. New approaches to strain selection and construction of beneficial microbial consortia should lead to more efficacious inoculant products. Extensive and rigorous field evaluation of inoculants under a range of soil and environmental conditions has rarely been undertaken and is urgently needed to validate emerging inoculant products and underpin successful implementation by growers, especially in a market that is largely unregulated at present.

P. Degnan, M. Taga, A. Goodman

L. Vuyst, S. V. Kerrebroeck, Henning Harth et al.

Riz Fernando Noronha, Kim Sneppen, Kunihiko Kaneko

Soil is a complex, dynamic material, with physical properties that depend on its biological content. We propose a cellular automaton model for self-organizing soil structure, where soil aggregates and serves as food for microbial species. These, in turn, produce nutrients that facilitate self-amplification, establishing a cyclical dynamic of consumption and regeneration. Our model explores the spatial interactions between these components and their role in sustaining a balanced ecosystem. The main results demonstrate that (1) spatial structure supports a stable living state, preventing population collapse or uncontrolled growth; (2) the spatial model allows for the coexistence of parasitic species, which exploit parts of the system without driving it to extinction; and (3) optimal growth conditions for microbes are associated to diverse length scales in the soil structure, suggesting that heterogeneity is key to ecosystem resilience. These findings highlight the importance of spatio-temporal dynamics of life in soil ecology.

Rylee Jensen, Erin A McKenney, James C Beasley et al.

The community of microbes in the gastrointestinal tract of mammals, known as the gut microbiome (GMB), plays a critical role in host ecology and evolution. GMB variation is modulated by both host physiology and environmental conditions experienced by the host. Here we characterized the GMBs of 11 free-ranging large herbivore species inhabiting Etosha National Park, Namibia. We examined how intrinsic (i.e., sex, gut morphology, feeding guild) and extrinsic (i.e., geographic zone, waterhole site) factors influenced GMB diversity and community structure within and across herbivore species. We extracted DNA from herbivore fecal samples (n = 312) and amplified the 16s rRNA gene region to identify bacterial taxa. We defined core bacterial taxa as those present at ≥1% relative abundance in ≥50% of the samples from each species. Within bovid species, the core phylum Verrucomicrobiota and the core genera RF39, Alistipes, Christensenellaceae_R-7 group, and NK4A214 were significantly different in abundance across geographic zones. Microbial richness was significantly greater in female than male eland, and we detected sex-specific differences in Christensenellaceae_R-7 group across all herbivores and P-251-O5 within gemsbok. Mean Bulla evenness was higher in ruminants than nonruminants and differed significantly between giraffes and impala. Elephants also showed a significant correlation between unweighted UniFrac distance and geographic distance between sample locations. By identifying baseline core microbial abundance and occurrence data for this herbivore community, wildlife managers can incorporate long-term GMB monitoring to track microbial shifts in host species over time.

Reilly Pidgeon, Arianna Giurleo, Lharbi Dridi et al.

Abstract Urolithins are a class of bioactive metabolites derived from the metabolism of dietary ellagitannins by the human gut microbiota. In the gut, urolithins are dehydroxylated regioselectively based on microbiota composition and activity. A single 9-hydroxy urolithin dehydroxylase (ucd) operon in gut resident Enterocloster species has been described to date; however, most enzymes in the urolithin metabolic pathway remain uncharacterized. Here, we investigate urolithin cross-feeding between members of the gut microbiota and discover a novel urolithin dehydroxylase in a subset of Enterocloster species. We show that urolithin intermediates, released by gut resident Gordonibacter species during ellagic acid metabolism, are dehydroxylated at both the 9- and 10-positions by E. asparagiformis, E. citroniae, and E. pacaense, but not E. bolteae. Using untargeted proteomics, we uncover a 10-hydroxy urolithin dehydroxylase operon, termed uxd, responsible for these species-specific differences in urolithin metabolism. By inducing uxd expression with diverse urolithins, we show that 9-hydroxy urolithins are required for uxd transcription and 10-position dehydroxylation. Collectively, this study reveals some of the genes, proteins, and substrate features underlying differences in urolithin metabolism by the human gut microbiota.

Robert C. Hill, Aleksandra Pieńkowska, Ines Merbach et al.

Fertilizers are widely used to sustain food production but can alter soil chemistry and potentially contribute toxic metal(loid)s to agricultural systems. For the first time, this study examined the occurrence of select metal(loid)s (Zn, Sr, V, As, Cd, Pb, and U) alongside the 87Sr/86Sr isotope ratio in agricultural soil– both total and mobile pools– and wheat grain. Samples were collected from one of four fertilization treatments– mineral (NPK), organic (manure), combined mineral+organic, and unfertilized controls– within the 120-year Static Fertilization Experiment in Bad Lauchstädt, Germany. Fertilization treatments altered soil pH and organic carbon resulting in mineral fertilization lowering pH and increasing cation mobility (Cd, Zn, Sr), whereas organic fertilization increased pH and enhanced the mobility of non-cationic elements (V, As). These effects translated into higher Cd in mineral-fertilized wheat grain and higher As in mineral+organic wheat grain. Fertilization shifted the 87Sr/86Sr ratios in soils and wheat grains toward that of the applied fertilizers, with mineral and mineral+organic wheat grains inheriting the triple super phosphate signature (0.70778) and organic wheat grains matching manure (0.70883). The 87Sr/86Sr ratio in the mobile soil pool was correlated with mobile As, V, and P, demonstrating that the 87Sr/86Sr ratio reflects both fertilizer source and the mobility of select co-occurring metal(loid)s. Overall, this study demonstrates metal(loid) enrichment in soil and wheat from fertilization and establishes 87Sr/86Sr ratio as a robust tracer of fertilizer impacts. These findings underscore the need for targeted fertilization strategies to reduce contaminant accumulation in agroecosystems.

Kelsey M. Wheeler, Myung Whan Oh, Julianna Fusco et al.

Infections often occur in complex niches consisting of multiple bacteria. Despite the increasing awareness, there is a fundamental gap in understanding which interactions govern microbial community composition. <i>Pseudomonas aeruginosa</i> is frequently isolated from monomicrobial and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competition within co-cultures of <i>P. aeruginosa</i> and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of <i>P. aeruginosa</i> against other ESKAPEE pathogens and the contribution of this pathogen’s multiple quorum-sensing (QS) systems in these interactions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in <i>P. aeruginosa</i> virulence. Using a collection of <i>P. aeruginosa</i> QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI, and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR, control competition between <i>P. aeruginosa</i> and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of <i>P. aeruginosa</i> with the ESKAPEE pathogens tested while disarming the pathogens’ ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously attenuating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.

P. Buttigieg, A. Ramette

R. M. Braga, M. N. Dourado, W. L. Araújo

The microorganism–microorganism or microorganism–host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial–host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community.

Fayyaz Ali Shah, Q. Mahmood, Mohammad Maroof Shah et al.

Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO2. The conversions of complex organic compounds to CH4 and CO2 are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.

Mattia Mattei, Alex Arenas

This study investigates the role of spatial segregation, prompted by competition avoidance, as a key mechanism for emergent coexistence within microbial communities. Recognizing these communities as complex adaptive systems, we challenge the sufficiency of mean-field pairwise interaction models and consider the impact of spatial dynamics. We developed an individual-based spatial simulation depicting bacterial movement through a pattern of random walks influenced by competition avoidance, leading to the formation of spatially segregated clusters. This model was integrated with a Lotka-Volterra metapopulation framework focused on competitive interactions. Our findings reveal that spatial segregation combined with low diffusion rates and high compositional heterogeneity among patches can lead to emergent coexistence in microbial communities. This reveals a novel mechanism underpinning the formation of stable, coexisting microbe clusters, which is nonetheless incapable of promoting coexistence in the case of isolated pairs of species. This study underscores the importance of considering spatial factors in understanding the dynamics of microbial ecosystems.

Feniche Mohammed El, Gazzaz Hassane, Omari Hajar El et al.

Professional development plays a key role in improving laboratory quality management by enhancing staff skills and knowledge to implement and maintain the quality management system (QMS). This research aims to identify and prioritize continuing training needs for Moroccan laboratory professionals in QMS and to formulate recommendations for suitable training programs.