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 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 Evaluating host to host transplants as a method to study plant bacterial assembly

2021 ◽  
Author(s):  
Christopher M Baldock ◽  
Neil Wilson ◽  
Rosalind Deaker
Keyword(s):  
Community Assembly ◽  
Host Species ◽  
Bacterial Communities ◽  
Host Plants ◽  
Major Step ◽  
Ecological Processes ◽  
Surrogate Host ◽  
New Hosts ◽  
Species Specific ◽  
Microbiome Assembly

The ability to predict plant microbiome assembly will enable new bacterial-based technologies for agriculture. A major step towards this is quantifying the roles of ecological processes on community assembly. This is challenging, in part because individuals within a populations of host plants may be colonised by different assemblages of bacteria, simply because of variation in soil communities proximal to said plants. This creates uncertainty because it is difficult to estimate if the absence of a given species was a) because it was not present to colonise the plant or b) it went locally extinct from competition, predation or similar. To address this, the authors develop a mesocosm system to study bacterial communities of individual plants by replicated transplantation to a recipient host plant population, ensuring new hosts receive a homogenous species pool for colonisation. We sought to understand which factors affected the transplant and, what the main drivers of variation in the model communities were. A nested factorial design was used to investigate the transplantation of cultured or total, root or leaf associated bacterial communities from donor host species to surrogate host species. Specific metrics were developed to quantify colonisation efficiency of communities. The results show the root communities were more effectively transplanted than leaf communities, and a higher proportion of cultured communities were recovered than total communities. For root communities the strongest drivers of beta diversity was the donor host species, and for leaves it was the surrogate host species. Overall the results reveal that root, but not leaf communities are suited to this system reflecting their differing ecological drivers.

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 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 Bacterial Community Assembly in a Typical Estuarine Marsh with Multiple Environmental Gradients

2019 ◽  
Vol 85 (6) ◽  
Author(s):  
Zhiyuan Yao ◽  
Shicong Du ◽  
Chunling Liang ◽  
Yueji Zhao ◽  
Francisco Dini-Andreote ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Assembly ◽  
Salt Marshes ◽  
Bacterial Communities ◽  
Available Phosphorus ◽  
Rrna Gene ◽  
Gradient System ◽  
High Marsh ◽  
Ecological Processes ◽  
Topological Features

ABSTRACTBacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly is poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high marsh, using 16S rRNA gene amplicon sequencing. Bacterial community compositions differed significantly between sediment transects. Physicochemical properties, particularly sediment nutrient levels (i.e., total nitrogen [TN] and available phosphorus [AP]), as well as sediment physical structure and pH (P < 0.05), were strongly associated with the overall community variations. In addition, the topological properties of bacterial cooccurrence networks varied with distance to the water-land junction. Both node- and network-level topological features revealed that the bacterial network of sediments farthest from the junction was less intense in complexity and interactions than other sediments. Phylogenetic null modeling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, data from this study provide a detailed outline of the distribution pattern of the sediment bacterial community across an estuarine marsh and inform the mechanisms and processes mediating bacterial community assembly in marsh soils.IMPORTANCESalt marshes represent highly dynamic ecosystems where the atmosphere, continents, and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating bacterial assembly are poorly understood for salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of bacterial communities in an estuarine marsh located in south Hangzhou Bay were investigated. The results revealed an intricate interplay between stochastic and deterministic processes mediating the assembly of bacterial communities in the studied gradient system. Collectively, our findings illustrate the main drivers of community assembly, taking into consideration changes in sediment abiotic variables and potential biotic interactions. Thus, we offer new insights into estuarine bacterial communities and illustrate the interplay of ecological processes shaping the assembly of bacterial communities in estuarine marsh ecosystems.

scholarly journals Response of gut microbiota to feed-borne bacteria depends on fish growth rate: a snapshot survey of farmed juvenile Takifugu obscurus

2020 ◽  
Author(s):  
Xingkun Jin ◽  
Ziwei Chen ◽  
Yan Shi ◽  
Jian-Fang Gui ◽  
Zhe Zhao
Keyword(s):  
Growth Rate ◽  
Gut Microbiota ◽  
Slow Growth ◽  
Ecological Processes ◽  
Associated Bacteria ◽  
Microbe Interactions ◽  
Environmental Bacteria ◽  
Feed Source ◽  
Host Microbe Interactions ◽  
Insight Into

ABSTRACTUnderstanding the ecological processes in controlling the assemblage of gut microbiota becomes an essential prerequisite for a more sustainable aquaculture. Here we used 16S rRNA amplicon sequencing to characterize the hindgut microbiota from cultured obscure puffer Takifugu obscurus. The gut microbiota is featured with lower alpha-diversity, greater beta-dispersion and higher average 16S rRNA copy numbers comparing to water and sediment, but far less so to feed. SourceTracker predicted a notable source signature from feed in gut microbiota. Furthermore, effect of varying degrees of feed-associated bacteria on compositional, functional and phylogenetic diversity of gut microbiota were revealed. Coincidently, considerable increase of species richness and feed source proportions both were observed in slow growth fugu, implying a reduced stability in gut microbiota upon bacterial disturbance from feed. Moreover, quantitative ecological analytic framework was applied and the ecological processes underlying such community shift were determined. In the context of lower degree of feed disturbance, homogeneous selection and dispersal limitation largely contribute to the community stability and partial variations among hosts. Whilst with the degree of feed disturbance increased, variable selection leads to an augmented interaction within gut microbiota, entailing community unstability and shift. Altogether, our findings illustrated a clear diversity-function relationships in fugu gut microbiota, and it has implicated in a strong correlation between feed-borne bacteria and host growth rate. These results provide a new insight into aquaculture of fugu and other economically important fishes, as well as a better understanding of host-microbe interactions in the vertebrate gastrointestinal tract.IMPORTANCEEnvironmental bacteria has a great impact on fish gut microbiota, yet little is known as to where fish acquire their gut symbionts, and how gut microbiota response to environmental bacteria. Through the integrative analysis by community profiling and source tracking, we show that feed-associated bacteria can impose a strong disturbance upon fugu gut microbiota. As a result, marked alterations in the composition and function of gut microbiota in slow growth fugu were observed, which is potentially correlated with the host physiological condition such as gastric evacuation rate. Our findings emphasized the intricate linkage between feed and gut microbiota, and highlighted the importance of resolving the feed source signal before the conclusion of comparative analysis of microbiota can be drawn. Our results provide a deeper insight into aquaculture of fugu and other economically important fishes, and have further implications for an improved understanding of host-microbe interactions in the vertebrate gastrointestinal tract.

scholarly journals Heritable associations with microbial communities are essential for necrotrophic pathogen resistance

2020 ◽  
Author(s):  
Cloe S. Pogoda ◽  
Stephan Reinert ◽  
Zahirul I. Talukder ◽  
Ziv Attia ◽  
Jason A. Corwin ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Microbial Communities ◽  
Genetic Architecture ◽  
Pathogen Resistance ◽  
Heritable Variation ◽  
Ecological Processes ◽  
Necrotrophic Pathogen ◽  
Microbe Interactions ◽  
Microbial Associations ◽  
Host Microbe Interactions

AbstractHost-microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity, and community-scale ecological processes. However, less is known about how genetic variation affects hosts’ associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbors substantial, heritable variation in microbial communities under field conditions. We show that microbial communities explain up to 77.5% of the heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum, and that plants grown in sterilized soil showed almost complete elimination of pathogen resistance. Association mapping revealed 69 genetic locations related to microbial abundance and Sclerotinia resistance. Although the genetic architecture is complex and quantitative, we have, in large part, elucidated previously unexplained genetic variation for resistance to this pathogen. This suggests new targets for plant breeding and demonstrates the potential for heritable microbial associations to play important roles in defense in natural and human-altered environments.

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