Hasil untuk "Microbial ecology"

A. Shade, H. Peter, S. Allison et al.

Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives – informed by meta-omics data – may provide about microbial community stability.

E. Paul

K. Rabaey, N. Boon, S. Siciliano et al.

M. Oshiki, H. Satoh, S. Okabe

Jim A. Harris

P. Galand, E. Casamayor, D. Kirchman et al.

Zhenting Xiang, Zi Wang, Nikoo Ghasemi et al.

Background The oral cavity presents a highly dynamic environment where inter-microbial communications play a pivotal role. Understanding the spatial organization of microbial ecosystems has been highlighted on the microbiome and polymicrobial infection. Furthermore, cross-feeding and modulation by metabolites from the oral microbiota and host cells, such as lactate and reactive oxidative species, impact the stability and functionality of microbial communities. Traditional research focusing solely on the compositional aspects of these communities is insufficient to understand the sophisticated interactions.Methods We evaluated recent advancements in imaging technologies, bolstered by multi-omics analyses and artificial intelligence (AI)-driven approachesinsights, to provide an more integrated understanding of the dynamics and function of the oral microbiome.Results Real time imaging and resolution-enhancing methods at the single-cell level have unraveled the ecology and dynamics of microbial communities, indicating unique three-dimensional architectures and biogeographical patterns associated with disease status in polymicrobial interplays. Emerging computational techniques can account for the spatial features of oral microbiome by creating image-like representations that capture the complex relationships between host tissues and microbial communities. Spatial multi-omics, help address the limitations of single-cell sequencing, deciphering molecular mechanisms between species in these biogeographical patterns. To process the massive volume of imaging-based data, AI-assisted analysis enables complex dataset integration, predictive capacity, and personalized treatment, bringing a whole new level of understanding of the oral microbiome and its relationships with the host.Conclusion In this review, we highlight recent imaging-based technologies used to study the spatial biogeography of interspecies and interkingdom relationships within oral microbial communities, focusing on how these interactions and functional/metabolic alterations associated with health and disease. We further outline limitations of AI-generated predictions and imaging-based observational data. Finally, we elaborate on potential biomarkers for early diagnosis and new effective therapeutic strategies to reshape microbial dynamics.

Shaohua Gu, Jiqi Shao, Ruolin He et al.

Abstract Iron is a critical yet limited nutrient for microbial growth. To scavenge iron, most microbes produce siderophores—diverse small molecules with high iron affinities. Different siderophores are specifically recognized and uptaken by corresponding recognizers, enabling targeted interventions and intriguing cheater‐producer dynamics. We propose constructing a comprehensive iron interaction network, or “iron‐net”, across the microbial world. Such a network offers the potential for precise manipulation of the microbiota, with conceivable applications in medicine, agriculture, and industry as well as advancing microbial ecology and evolution theories. Previously, our successful construction of an iron‐net in the Pseudomonas genus demonstrated the feasibility of coevolution‐inspired digital siderophore‐typing. Enhanced by machine learning techniques and expanding sequencing data, forging such an iron‐net calls for multidisciplinary collaborations and holds significant promise in addressing critical challenges in microbial communities.

Vincent Raquin, Edwige Martin, Guillaume Minard et al.

Abstract Background Ecological niches present unique environmental and biological trademarks such as abiotic conditions, nutrient availability, and trophic interactions that may impact the ecology of living organisms. Female mosquitoes deposit their eggs in aquatic niches with fluctuating diet sources and microbial communities. However, how niche’s diet and microbial composition impact mosquito performance (i.e., traits that maximize mosquito fitness) are not well understood. In this study, we focused on the Asian tiger mosquito, Aedes albopictus, one of the most invasive species in the world and a competent vector for human pathogens. To remove any external microbes, Ae. albopictus eggs were surface-sterilized then hatching larvae were exposed to a gradient of bacterial inoculum (i.e., initial microbial load) and diet concentrations while their impact on mosquito performance traits during juvenile development was measured. Results Our results showed that Ae. albopictus larvae develop faster and give larger adults when exposed to microbiota in rearing water. However, mosquito performance, up to the adult stage, depends on both bacterial inoculum size and diet concentration in the aquatic habitat. Upon low inoculum size, larvae survived better if the diet was in sufficient amounts whereas a higher inoculum size was associated with optimal larvae survival only in the presence of the lower amount of diet. Inoculum size, and to a lesser extent diet concentration, shaped bacterial community structure and composition of larval-rearing water allowing the identification of bacterial taxa for which their abundance in larvae-rearing water correlated with niche parameters and/or larval traits. Conclusions Our work demonstrates that both diet concentration and bacterial inoculum size impact mosquito performance possibly by shaping bacterial community structure in the larval habitat, which accounts for a large part of the juvenile’s microbiota. Host-microbe interactions influence several mosquito life-history traits, and our work reveals that niche parameters such as inoculum size and diet concentration could have numerous implications on the microbiota assembly and host evolutionary trajectory. This underlies that host-microbe-environment interactions are an important yet overlooked factor of mosquito adaptation to its local environment, with potential future implications for vector control and vector ecology. Video Abstract

Mingming Yang, Daniel C. Schlatter, Melissa K. LeTourneau et al.

Plants and their associated microbiomes are impacted by environmental factors that shape their interactions over time, but long-term trends in microbial community dynamics are not well characterized. We identified the seasonal and long-term population dynamics of root-associated bacterial communities over 8 years in monocropped wheat grown in adjacent dryland and irrigated plots in the low-precipitation region of Washington State. Spring wheat plants were sampled at various times during the growing season over 8 years, and rhizosphere and endosphere communities were characterized using 16S rRNA amplicon sequencing. Analyses throughout the first 3 years revealed genera with distinct annual periodicity in response to growing season conditions. Bacterial richness and diversity were significantly greater in irrigated than in dryland wheat and in the rhizosphere than in the endosphere, apparently driven by the physiological state of the root and root exudates and/or by soil water. Over 8 years, copiotrophic Proteobacteria and Bacteroidetes (Pseudomonas, Variovorax, Chryseobacterium) maintained stable populations, whereas Actinobacteria decreased in abundance independent of irrigation. Populations of some Bacteroidetes and Proteobacteria (Mucilaginibacter, Sphingomonas, Massilia, Burkholderia) persisted or increased in relative abundance in the dryland rhizosphere, whereas others (Rhizobium, Acidovorax, Terrimonas, Hyphomicrobium, Bdellovibrio) increased under irrigation. In contrast, endosphere taxa, including Actinobacteria, declined in relative abundance regardless of irrigation, indicating that the maturing host, and not water, is the main driver of these populations. Our results provide insight into the long-term dynamics of bacterial communities of wheat under contrasting soil water conditions and guide future efforts to improve crop performance under drought conditions. [Figure: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.

Celia Díez López, Florence Van Herreweghen, Britta De Pessemier et al.

Abstract Background Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents in laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation and negative impacts on consumer well-being. Clothing undergoes cycles of wearing, washing and drying, with variable exposure to microorganisms and volatilomes originating from the skin, washing machine, water and laundry products. Laundry malodour is therefore a complex problem that reflects its dynamic ecosystem. To date, comprehensive investigations that encompass the evaluation of both microbial community and malodorous volatile organic compounds throughout all stages of the wash-wear-dry cycle are scarce. Furthermore, the microbial and malodour profiles associated with extended humid-drying conditions are poorly defined. Results Here we present olfaction-directed chemical and microbiological studies of synthetic T-shirts after wearing, washing and drying. Results show that although washing reduces the occurrence of known malodour volatile organic compounds, membrane-intact bacterial load on clothing is increased. Skin commensals are displaced by washing machine microbiomes, and for the first time, we show that this shift is accompanied by an altered pathogenomic profile, with many genes involved in biofilm build-up. We additionally highlight that humid-drying conditions are associated with characteristic malodours and favour the growth of specific Gram-negative bacteria. Conclusions These findings have important implications for the development of next-generation laundry products that enhance consumer well-being, while supporting environmentally friendly laundry practices.

Zhishu Wang, Jianyu Xiao, Fusong Han et al.

A rapid increase in nitrogen deposition has caused many hazards to the Tibetan Plateau over the past few decades. However, as one of the important limiting factors in alpine ecosystems, nitrogen fertilizers are often used to restore the severely degraded grassland. But, little is known about the response of soil microbes to nitrogen addition in the western Tibetan, which will limit our understanding and comprehensive assessment of global alpine grassland ecosystems. This study conducted an experiment with five levels of nitrogen addition (0, 5, 10, 20, 40 g N m⁻² y⁻¹) in an alpine steppe (AS) and an alpine desert steppe (ADS) at the source of Brahmaputra. In this study, plant and soil data were analyzed from August 2023, it showed that nitrogen sensitivity of soil microbes and their response to nitrogen addition vary with the nitrogen addition rate, grassland type, microbial kingdom, and the dimension used. Nitrogen sensitivity of soil bacterial community in the AS was higher than that in the ADS at 10 g N m⁻² y⁻¹ nitrogen addition rate, while the result was reversed at 20–40 g N m⁻² y⁻¹ ; the fungal community was more sensitive than bacterial community in the ADS at 5 g N m⁻² y⁻¹ nitrogen addition rate, while the result was reversed 20–40 g N m⁻² y⁻¹ ; the nitrogen sensitivity of the bacterial community's β-diversity in AS varied across species, functional, and phylogenetic dimensions. The main environment factors affecting nitrogen sensitivity were different in the AS and the ADS. This study explored the effects of nitrogen addition on soil bacterial and fungal communities in two types of grasslands in the western Tibetan, providing important foundations for further understanding of microbial ecology in alpine ecosystems, as well as valuable insights for managing nitrogen deposition in alpine ecosystems.

Yunshi Li, Ling Jin, Minghui Wu et al.

Research has shown that forest management can improve the post-drought growth and resilience of Qinghai spruce in the eastern Qilian Mountains, located on the northeastern Tibetan Plateau. However, the impact of such management on the tree-associated phyllosphere microbiome is not yet fully understood. This study provides new evidence of positive forest management effects on the phyllosphere microbiome after extreme drought, from the perspectives of community diversity, structure, network inference, keystone species, and assembly processes. In managed Qinghai spruce forest, the α-diversity of the phyllosphere bacterial communities increased, whereas the β-diversity decreased. In addition, the phyllosphere bacterial community became more stable and resistant, yet less complex, following forest management. Keystone species inferred from a bacterial network also changed under forest management. Furthermore, forest management mediated changes in community assembly processes, intensifying the influence of determinacy, while diminishing that of stochasticity. These findings support the hypothesis that management can re-assemble the phyllosphere bacterial community, enhance community stability, and ultimately improve tree growth. Overall, the study highlights the importance of forest management on the phyllosphere microbiome and furnishes new insights into forest conservation from the perspective of managing microbial processes and effects.

Ulises E. Rodríguez-Cruz, Ulises E. Rodríguez-Cruz, Hugo G. Castelán-Sánchez et al.

A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the “Archaean Domes” (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5–9.8) and high salinity (5.28% to saturation).

Wei Ge, Yulian Ren, Chunbo Dong et al.

Cantharellus cibarius, an ectomycorrhizal fungus belonging to the Basidiomycetes, has significant medicinal and edible value, economic importance, and ecological benefits. However, C. cibarius remains incapable of artificial cultivation, which is thought to be due to the presence of bacteria. Therefore, much research has focused on the relationship between C. cibarius and bacteria, but rare bacteria are frequently overlooked, and symbiotic pattern and assembly mechanism of the bacterial community associated with C. cibarius remain unknown. In this study, the assembly mechanism and driving factors of both abundant and rare bacterial communities of C. cibarius were revealed by the null model. The symbiotic pattern of the bacterial community was examined using a co-occurrence network. Metabolic functions and phenotypes of the abundant and rare bacteria were compared using METAGENassist2, and the impacts of abiotic variables on the diversity of abundant and rare bacteria were examined using partial least squares path modeling. In the fruiting body and mycosphere of C. cibarius, there was a higher proportion of specialist bacteria compared with generalist bacteria. Dispersal limitation dominated the assembly of abundant and rare bacterial communities in the fruiting body and mycosphere. However, pH, 1-octen-3-ol, and total phosphorus of the fruiting body were the main driving factors of bacterial community assembly in the fruiting body, while available nitrogen and total phosphorus of the soil affected the assembly process of the bacterial community in the mycosphere. Furthermore, bacterial co-occurrence patterns in the mycosphere may be more complex compared with those in the fruiting body. Unlike the specific potential functions of abundant bacteria, rare bacteria may provide supplementary or unique metabolic pathways (such as sulfite oxidizer and sulfur reducer) to enhance the ecological function of C. cibarius. Notably, while volatile organic compounds can reduce mycosphere bacterial diversity, they can increase fruiting body bacterial diversity. Findings from this study further, our understanding of C. cibarius-associated microbial ecology.

Anaïs K. Tallon, Lee-Anne Manning, Flore Mas

The Queensland fruit fly (<i>Bactrocera tryoni</i>) is a major polyphagous pest widespread in Australia and several Pacific Islands. Bacteria present on the host plant phyllosphere supply proteins, essential for egg development and female sexual maturity. We investigated the role of microbial volatile organic compounds (MVOCs) emitted by Enterobacteriaceae commonly found on the host plant and in the fly gut in attracting virgin females. Bacteria were cultured on artificial media and natural fruits, at various pH, and MVOCs were collected using different headspace volatile absorbent materials. The olfactory responses of virgin females to bacterial MVOCs were assessed via electrophysiology and behavioral assays. The production of MVOCs was strongly influenced qualitatively by the bacterial strain and the type of media, and it semi-quantitatively varied with pH and time. MVOCs emitted by <i>Klebsiella oxytoca</i> invoked the strongest antennal response and were the most attractive. Among the identified compounds triggering an olfactory response, D-limonene and 2-nonanone were both significantly behaviorally attractive, whereas phenol, nonanal, isoamyl alcohol, and some pyrazines appeared to be repulsive. This study deepens our understanding of the chemical ecology between fruit flies and their bacterial symbionts and paves the way for novel synthetic lures based on specifically MVOCs targeting virgin females.

J. Gilbert, S. Lynch

Diana M Proctor, D. Relman

Landscape ecology examines the relationships between the spatial arrangement of different landforms and the processes that give rise to spatial and temporal patterns in local community structure. The spatial ecology of the microbial communities that inhabit the human body-in particular, those of the nose, mouth, and throat-deserves greater attention. Important questions include what defines the size of a population (i.e., "patch") in a given body site, what defines the boundaries of distinct patches within a single body site, and where and over what spatial scales within a body site are gradients detected. This Review looks at the landscape ecology of the upper respiratory tract and mouth and seeks greater clarity about the physiological factors-whether immunological, chemical, or physical-that govern microbial community composition and function and the ecological traits that underlie health and disease.

Emily G. Simmonds, Kwaku Peprah Adjei, Christoffer Wold Andersen et al.

Summary: Quantifying uncertainty associated with our models is the only way we can express how much we know about any phenomenon. Incomplete consideration of model-based uncertainties can lead to overstated conclusions with real-world impacts in diverse spheres, including conservation, epidemiology, climate science, and policy. Despite these potentially damaging consequences, we still know little about how different fields quantify and report uncertainty. We introduce the “sources of uncertainty” framework, using it to conduct a systematic audit of model-related uncertainty quantification from seven scientific fields, spanning the biological, physical, and political sciences. Our interdisciplinary audit shows no field fully considers all possible sources of uncertainty, but each has its own best practices alongside shared outstanding challenges. We make ten easy-to-implement recommendations to improve the consistency, completeness, and clarity of reporting on model-related uncertainty. These recommendations serve as a guide to best practices across scientific fields and expand our toolbox for high-quality research.

Zhenghu Zhou, Chuankuan Wang, Lifen Jiang et al.