scholarly journals Host-associated fungal communities are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome

2020 ◽  
Author(s):  
Xavier A. Harrison ◽  
Allan D. McDevitt ◽  
Jenny C. Dunn ◽  
Sarah Griffiths ◽  
Chiara Benvenuto ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Natural Populations ◽  
Fungal Communities ◽  
Phylogenetic Distance ◽  
Bacterial Microbiome ◽  
Host Phylogeny ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Microbial Groups ◽  
Taxonomic Groups

ABSTRACTInteractions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Despite a recent proliferation of research on interactions between animals and their associated bacterial communities, comparative evidence from fungal communities is lacking, especially in natural populations. This disparity means knowledge of host-microbe interactions is biased towards the bacterial microbiome. Using samples from 49 species from eight metazoan classes, we demonstrate that the ecological distance between both fungal and bacterial components of the microbiome shift in tandem with host phylogenetic distance. Though so-called phylosymbiosis has been shown in bacterial communities, we extend previous knowledge by demonstrating that the magnitude of shifts in fungal and bacterial community structure across host phylogeny are correlated. These data are indicative of coordinated recruitment by hosts for specific suites of microbes, and potentially selection for bacterial-fungal interactions across a broad taxonomic range of host species. Using co-occurrence networks comprising both microbial groups, we illustrate that fungi form a critical component of microbial interaction networks, and that the strength and frequency of such interactions vary across host taxonomic groups. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.

scholarly journals Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome

2021 ◽  
Vol 288 (1957) ◽  
pp. 20210552
Author(s):  
Xavier A. Harrison ◽  
Allan D. McDevitt ◽  
Jenny C. Dunn ◽  
Sarah M. Griffiths ◽  
Chiara Benvenuto ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Natural Populations ◽  
Sample Type ◽  
Fungal Community Composition ◽  
Tissue Storage ◽  
Bacterial Microbiome ◽  
Host Phylogeny ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Using Data

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host–microbe interactions.

scholarly journals Pseudomonas Lipopeptide-Mediated Biocontrol: Chemotaxonomy and Biological Activity

Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 372
Author(s):  
Feyisara Eyiwumi Oni ◽  
Qassim Esmaeel ◽  
Joseph Tobias Onyeka ◽  
Rasheed Adeleke ◽  
Cedric Jacquard ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
In Vitro Assays ◽  
Bacterial Physiology ◽  
Lineage Specificity ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
The One ◽  
Taxonomic Groups ◽  
Plant Pathogen Interactions

Pseudomonas lipopeptides (Ps-LPs) play crucial roles in bacterial physiology, host–microbe interactions and plant disease control. Beneficial LP producers have mainly been isolated from the rhizosphere, phyllosphere and from bulk soils. Despite their wide geographic distribution and host range, emerging evidence suggests that LP-producing pseudomonads and their corresponding molecules display tight specificity and follow a phylogenetic distribution. About a decade ago, biocontrol LPs were mainly reported from the P. fluorescens group, but this has drastically advanced due to increased LP diversity research. On the one hand, the presence of a close-knit relationship between Pseudomonas taxonomy and the molecule produced may provide a startup toolbox for the delineation of unknown LPs into existing (or novel) LP groups. Furthermore, a taxonomy–molecule match may facilitate decisions regarding antimicrobial activity profiling and subsequent agricultural relevance of such LPs. In this review, we highlight and discuss the production of beneficial Ps-LPs by strains situated within unique taxonomic groups and the lineage-specificity and coevolution of this relationship. We also chronicle the antimicrobial activity demonstrated by these biomolecules in limited plant systems compared with multiple in vitro assays. Our review further stresses the need to systematically elucidate the roles of diverse Ps-LP groups in direct plant–pathogen interactions and in the enhancement of plant innate immunity.

scholarly journals Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Ragnhild I Vestrum ◽  
Kari J K Attramadal ◽  
Olav Vadstein ◽  
Madeleine Stenshorne Gundersen ◽  
Ingrid Bakke
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Atlantic Cod ◽  
Animal Health ◽  
Striking Difference ◽  
Ecological Processes ◽  
Opportunistic Bacteria ◽  
Atlantic Cod Larvae ◽  
Microbe Interactions ◽  
Host Microbe Interactions

ABSTRACT Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host–microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host–microbe interactions and improved fish health and survival.

scholarly journals Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7715 ◽  
Author(s):  
Ze Ren ◽  
Hongkai Gao
Keyword(s):  
Microbial Communities ◽  
Central Asia ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Vegetation Index ◽  
Hydrological Modeling ◽  
Alpha Diversity ◽  
Environmental Variation ◽  
Fungal Communities ◽  
Taxonomic Groups

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

scholarly journals Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster

2019 ◽  
Vol 116 (40) ◽  
pp. 20025-20032 ◽  
Author(s):  
Seth M. Rudman ◽  
Sharon Greenblum ◽  
Rachel C. Hughes ◽  
Subhash Rajpurohit ◽  
Ozan Kiratli ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Populations ◽  
Microbiome Composition ◽  
Adaptive Process ◽  
Population Genomic ◽  
Polygenic Adaptation ◽  
Microbial Group ◽  
Genomic Adaptation ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Population genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such patterns is challenging; it requires disentangling the ecological agents of selection, determining the relevant timescales over which evolution occurs, and elucidating the genetic architecture of adaptation. Doing so for the adaptation of hosts to their microbiome is of particular interest with growing recognition of the importance and complexity of host–microbe interactions. Here, we track the pace and genomic architecture of adaptation to an experimental microbiome manipulation in replicate populations of Drosophila melanogaster in field mesocosms. Shifts in microbiome composition altered population dynamics and led to divergence between treatments in allele frequencies, with regions showing strong divergence found on all chromosomes. Moreover, at divergent loci previously associated with adaptation across natural populations, we found that the more common allele in fly populations experimentally enriched for a certain microbial group was also more common in natural populations with high relative abundance of that microbial group. These results suggest that microbiomes may be an agent of selection that shapes the pattern and process of adaptation and, more broadly, that variation in a single ecological factor within a complex environment can drive rapid, polygenic adaptation over short timescales.

scholarly journals Old and new models for studying host-microbe interactions in health and disease:C. difficileas an example

2017 ◽  
Vol 312 (6) ◽  
pp. G623-G627 ◽  
Author(s):  
Vincent B. Young
Keyword(s):  
Human Health ◽  
Bacterial Communities ◽  
Human Microbiome ◽  
Model Systems ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Indigenous Microbiota ◽  
Pathogenic Microbes ◽  
Host Microbe Interactions ◽  
Insight Into

There has been an explosion of interest in studying the indigenous microbiota, which plays an important role in human health and disease. Traditionally, the study of microbes in relationship to human health involved consideration of individual microbial species that caused classical infectious diseases. With the interest in the human microbiome, an appreciation of the influence that complex communities of microbes can have on their environment has developed. When considering either individual pathogenic microbes or a symbiotic microbial community, researchers have employed a variety of model systems with which they can study the host-microbe interaction. With the use of studies of infections with the toxin-producing bacterium Clostridium difficile as a model for both a pathogen and beneficial bacterial communities as an example, this review will summarize and compare various model systems that can be used to gain insight into the host-microbe interaction.

Seasonal dynamics of Chironomus transvaalensis populations and the microbial community composition of their egg masses

2019 ◽  
Vol 366 (24) ◽  
Author(s):  
Rotem Sela ◽  
Malka Halpern
Keyword(s):  
Bacterial Communities ◽  
Microbial Community Composition ◽  
Egg Mass ◽  
Egg Masses ◽  
Predator Prey ◽  
Gelatinous Matrix ◽  
Prey Interaction ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Freshwater Environments

ABSTRACT Chironomids (Diptera; Chironomidae) are the most abundant insects in freshwater environments and are considered natural reservoirs of Vibrio cholerae. We monitored the annual dynamics of chironomid populations along with their microbiota in order to better understand host–microbiota interactions. Chironomus transvaalensis populations peaked biannually in August and May–June. The composition of the endogenous bacterial communities of their egg masses clustered in two groups according to the sampling periods August–November and May–July. Nevertheless, a core bacterial community (43%) was present in all egg-mass samples. The most abundant phyla were: Proteobacteria, Firmicutes, Cyanobacteria and Bacteroidetes. The abundance of several genera (e.g. Rheinheimera and Pseudomonas) was positively correlated with C. transvaalensis population dynamics, while a predator–prey interaction was observed between the relative abundance of Vibrio OTUs and C. transvaalensis population size. Chironomids are known to tolerate toxic and stress conditions, and our results demonstrated that bacterial genera that may protect the insect under these conditions are present in the egg masses. After hatching, the first larval meal is the gelatinous matrix that surrounds the eggs. This meal contains a probiotic consortium that may protect the larva during its metamorphosis. The results provide important insights into the host–microbe interactions of chironomids.

scholarly journals Structural variability and differentiation of niches in the rhizosphere and endosphere bacterial microbiome of moso bamboo (Phyllostachys edulis)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zong-Sheng Yuan ◽  
Fang Liu ◽  
Zhen-Yu Liu ◽  
Qiu-Liang Huang ◽  
Guo-Fang Zhang ◽  
...  
Keyword(s):  
Nutrient Uptake ◽  
Rhizosphere Soil ◽  
Principal Component ◽  
Moso Bamboo ◽  
Hormone Balance ◽  
Bacterial Microbiome ◽  
Microbe Interactions ◽  
Development And Utilization ◽  
Plant Microbiota ◽  
Host Microbe Interactions

AbstractThe plant microbiota play a key role in plant productivity, nutrient uptake, resistance to stress and flowering. The flowering of moso bamboo has been a focus of study. The mechanism of flowering is related to nutrient uptake, temperature, hormone balance and regulation of key genes. However, the connection between microbiota of moso bamboo and its flowering is unknown. In this study, samples of rhizosphere soil, rhizomes, roots and leaves of flowering and nonflowering plants were collected, and 16S rRNA amplicon Illumina sequencing was utilized to separate the bacterial communities associated with different flowering stages of moso bamboo. We identified 5442 OTUs, and the number of rhizosphere soil OTUs was much higher than those of other samples. Principal component analysis (PCA) and hierarchical clustering (Bray Curtis dis) analysis revealed that the bacterial microorganisms related to rhizosphere soil and endophytic tissues of moso bamboo differed significantly from those in bulk soil and rhizobacterial and endosphere microbiomes. In addition, the PCA analyses of root and rhizosphere soil revealed different structures of microbial communities between bamboo that is flowering and not flowering. Through the analysis of core microorganisms, it was found that Flavobacterium, Bacillus and Stenotrophomonas played an important role in the absorption of N elements, which may affect the flowering time of moso bamboo. Our results delineate the complex host-microbe interactions of this plant. We also discuss the potential influence of bacterial microbiome in flowering, which can provide a basis for the development and utilization of moso bamboo.

scholarly journals H2-saturation of high affinity H2-oxidizing bacteria alters the ecological niche of soil microorganisms unevenly among taxonomic groups

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1782 ◽  
Author(s):  
Sarah Piché-Choquette ◽  
Julien Tremblay ◽  
Susannah G. Tringe ◽  
Philippe Constant
Keyword(s):  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Oxidation Activity ◽  
Soil Microbial ◽  
High Affinity ◽  
Correlation Networks ◽  
Soil Bacterial Community Structure ◽  
Microbe Interactions ◽  
Taxonomic Groups ◽  
The Impact

Soil microbial communities are continuously exposed to H2diffusing into the soil from the atmosphere. N2-fixing nodules represent a peculiar microniche in soil where H2can reach concentrations up to 20,000 fold higher than in the global atmosphere (0.530 ppmv). In this study, we investigated the impact of H2exposure on soil bacterial community structure using dynamic microcosm chambers simulating soil H2exposure from the atmosphere and N2-fixing nodules. Biphasic kinetic parameters governing H2oxidation activity in soil changed drastically upon elevated H2exposure, corresponding to a slight but significant decay of high affinity H2-oxidizing bacteria population, accompanied by an enrichment or activation of microorganisms displaying low-affinity for H2. In contrast to previous studies that unveiled limited response by a few species, the relative abundance of 958 bacterial ribotypes distributed among various taxonomic groups, rather than a few distinct taxa, was influenced by H2exposure. Furthermore, correlation networks showed important alterations of ribotype covariation in response to H2exposure, suggesting that H2affects microbe-microbe interactions in soil. Taken together, our results demonstrate that H2-rich environments exert a direct influence on soil H2-oxidizing bacteria in addition to indirect effects on other members of the bacterial communities.

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