Host relatedness influences the composition of aphid microbiomes.
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ABSTRACT:
SUBMITTER: McLean AHC
PROVIDER: S-EPMC6900097 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Animals and their microbiomes exert reciprocal influence; the host's environment, physiology, and phylogeny can impact the composition of the microbiome, while the microbes present can affect host behavior, health, and fitness. While some microbiomes are highly malleable, specialized microbiomes that provide important functions can be more robust to environmental perturbations. Recent evidence suggests Sceloporus virgatus has one such specialized microbiome, which functions to protect eggs from fungal pathogens during incubation. Here, we examine the cloacal microbiome of three different Sceloporus species (spiny lizards; Family Phrynosomatidae)-Sceloporus virgatus, Sceloporus jarrovii, and Sceloporus occidentalis. We compare two species with different reproductive modes (oviparous vs. viviparous) living in sympatry: S. virgatus and S. jarrovii. We compare sister species living in similar habitats (riparian oak-pine woodlands) but different latitudes: S. virgatus and S. occidentalis. And, we compare three populations of one species (S. occidentalis) living in different habitat types: beach, low elevation forest, and the riparian woodland. We found differences in beta diversity metrics between all three comparisons, although those differences were more extreme between animals in different environments, even though those populations were more closely related. Similarly, alpha diversity varied among the S. occidentalis populations and between S. occidentalis and S. virgatus, but not between sympatric S. virgatus and S. jarrovii. Despite these differences, all three species and all three populations of S. occcidentalis had the same dominant taxon, Enterobacteriaceae. The majority of the variation between groups was in low abundance taxa and at the ASV level; these taxa are responsive to habitat differences, geographic distance, and host relatedness. Uncovering what factors influence the composition of wild microbiomes is important to understanding the ecology and evolution of the host animals, and can lead to more detailed exploration of the function of particular microbes and the community as a whole.
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Project description:Host genotype and gender are among the factors that influence the composition of gut microbiota. We studied the population structure of gut microbiota in two lines of chickens maintained under the same husbandry and dietary regimes. The lines, which originated from a common founder population, had undergone 54 generations of selection for high (HW) or low (LW) 56-day body weight, and now differ by more than 10-fold in body weight at selection age. Of 190 microbiome species, 68 were affected by genotype (line), gender, and genotype by gender interactions. Fifteen of the 68 species belong to Lactobacillus. Species affected by genotype, gender, and the genotype by gender interaction, were 29, 48, and 12, respectively. Species affected by gender were 30 and 17 in the HW and LW lines, respectively. Thus, under a common diet and husbandry host quantitative genotype and gender influenced gut microbiota composite.
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Project description:Human modification of the environment, particularly through land-use change, often reduces animal species diversity. However, the effect of land-use change on the gut microbiome of wildlife in human-dominated landscapes is not well understood despite its potential consequences for host health. We sought to quantify the effect of land-use change on wild bird gut microbiomes in a countryside landscape in Costa Rica, comprising a range of habitat types, ranging from primary and secondary forests to diversified and monoculture farms. We collected 280 fresh fecal samples from individuals belonging to six common species of saltator, thrushes, and warblers at 24 sites across this land-use gradient. Through 16S rRNA community profiling, we found that bacterial species composition responded to host species identity more strongly than to habitat type. In addition, we found evidence that habitat type affected microbial composition only for two of the six bird species. Our findings indicate that some host species and their microbiota may be more vulnerable to human disturbances than others.
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Project description:The influence of gut microbiota on host immunity is widely studied, and its disturbance has been linked to several immune-mediated disorders. Conversely, whether and how inherently disturbed canonical Th1 (pro-inflammatory) and/or Th2 (anti-inflammatory) immune pathways modify the host microbiome is not sufficiently investigated. Here, we characterized the humoral, cellular, and cytokine immunity, and associated alterations in gut microbiota of naïve wild-type mice (C57BL/6 and BALB/c), and mice with deficiencies in Th2 responses (IL-4Rα and IL-33 knockout mice) or in both Th1 and Th2 responses (NOD scid gamma, NSG mice). A global analysis by de novo clustering of 16S rRNA profiles of the gut microbiota independently grouped wild-type immunocompetent (C57BL/6 and BALB/c), Th2-deficient (IL-4Rα-/- and IL-33-/-), and severely immunodeficient (NSG) mice; where wild-type mice, but not Th2 or severely immunodeficient mice, were enriched in gut bacteria that produce short-chain fatty acids. These include members of phyla Firmicutes, Verrucomicrobia, and Bacteroidetes such as Lactobacillus spp., Akkermansia muciniphila, and Odoribacter spp. Further comparison of the two naïve wild-type mouse strains showed higher microbial diversity (Shannon), primarily linked to higher richness (Chao1), as well as a distinct difference in microbial composition (weighted UniFrac) in BALB/c mice compared to C57BL/6. T-cell and blood cytokine analyses demonstrated a Th1-polarization in naïve adaptive immunity in C57BL/6 animals compared to BALB/c mice, and an expected Th2 deficient cellular response in IL-4Rα-/- and IL-33-/- mice compared to its genetic background BALB/c strain. Together, these data suggest that alterations in the Th1/Th2 balance or a complete ablation of Th1/Th2 responses can lead to major alterations in gut microbiota composition and function. Given the similarities between the human and mouse immune systems and gut microbiota, our finding that immune status is a strong driver of gut microbiota composition has important consequences for human immunodeficiency studies.
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Project description:BackgroundThe effect of soil on the plant microbiome is well-studied. However, less is known about the impact of the soil microbiome in multitrophic systems. Here we examined the effect of soil on plant and aphid microbiomes, and the reciprocal effect of aphid herbivory on the plant and soil microbiomes. We designed microcosms, which separate below and aboveground compartments, to grow oak seedlings with and without aphid herbivory in soils with three different microbiomes. We used amplicon sequencing and qPCR to characterize the bacterial and fungal communities in soils, phyllospheres, and aphids.ResultsSoil microbiomes significantly affected the microbial communities of phyllospheres and, to a lesser extent, aphid microbiomes, indicating plant-mediated assembly processes from soil to aphids. While aphid herbivory significantly decreased microbial diversity in phyllospheres independent of soil microbiomes, the effect of aphid herbivory on the community composition in soil varied among the three soils.ConclusionsThis study provides experimental evidence for the reciprocal influence of soil, plant, and aphid microbiomes, with the potential for the development of new microbiome-based pest management strategies.
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Project description:Aphids are serious agricultural insect pests which exploit the phloem sap of host plants and thus transmit pathogens to their hosts. However, the degree to which aphid parsitism affects the fitness of the host plants is not well understood. The aphid, Macrosiphoniella yomogicola, parasitizes the mugwort Artemisia montana in Japan. During summer most mugworts carry aphids, but most aphid colonies die out after the budding of A. montana inflorescences in late summer. A few aphid colonies survive to late autumn, at which point sexuparae appear to later lay overwintering eggs after copulation. The death of the aphid colonies seems to be caused by biochemical changes in the phloem sap in the host plant coincident with the budding of inflorescences. The surviving aphid colonies may suppress the budding of inflorescences to allow persistence of their genetic line into the following year. Our investigations demonstrate that aphid parasitism did not affect host plant growth, but that it did significantly decrease the number of inflorescences and the average weight of floral buds. Our results indicate that aphid parasitism has a strong negative effect on the fitness of host plants. The manner in which the aphids suppress floral budding in their hosts is worth examining from the perspective of the evolution of aphid-plant interactions.
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Project description:BackgroundLeaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant's defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with differing aphid resistance, grown in the same farmland.ResultsThe bacterial community in both the phyllosphere and endosphere showed significant differences among most wheat cultivars. The phyllosphere was connected to more complex and stable microbial networks than the endosphere in most wheat cultivars. Moreover, the genera Pantoea, Massilia, and Pseudomonas were found to play a major role in shaping the microbial community in the wheat phyllosphere. Additionally, wheat plants showed phenotype-specific associations with the genera Massilia and Pseudomonas. The abundance of the genus Exiguobacterium in the phyllosphere exhibited a significant negative correlation with the aphid hazard grade in the wheat plants.ConclusionCommunities of leaf-associated microbes in wheat plants were mainly driven by the host genotype. Members of the genus Exiguobacterium may have adverse effects on wheat aphids. Our findings provide new clues supporting the development of aphid control strategies based on phyllosphere microbiome engineering.
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Project description:Wildlife epidemiological outcomes can depend strongly on the composition of an ecological community, particularly when multiple host species are affected by the same pathogen. However, the relationship between host species richness and disease risk can vary with community context and with the degree of spillover transmission that occurs among co-occurring host species. We examined the degree to which host species composition influences infection by Batrachochytrium dendrobatidis (Bd), a widespread fungal pathogen associated with amphibian population declines around the world, and whether transmission occurs from one highly susceptible host species to other co-occurring host species. By manipulating larval assemblages of three sympatric amphibian species in the laboratory, we characterized the relationship between host species richness and infection severity, whether infection mediates growth and survivorship differently across various combinations of host species, and whether Bd is transmitted from experimentally inoculated tadpoles to uninfected tadpoles. We found evidence of a dilution effect where Bd infection severity was dramatically reduced in the most susceptible of the three host species (Anaxyrus boreas). Infection also mediated survival and growth of all three host species such that the presence of multiple host species had both positive (e.g., infection reduction) and negative (e.g., mortality) effects on focal species. However, we found no evidence that Bd infection is transmitted by this species. While these results demonstrate that host species richness as well as species identity underpin infection dynamics in this system, dilution is not the product of reduced transmission via fewer infectious individuals of a susceptible host species. We discuss various mechanisms, including encounter reduction and antagonistic interactions such as competition and opportunistic cannibalism that may act in concert to mediate patterns of infection severity, growth, and mortality observed in multihost communities.
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Project description:BackgroundUnderstanding the factors regulating our microbiota is important but requires appropriate statistical methodology. When comparing two or more populations most existing approaches either discount the underlying compositional structure in the microbiome data or use probability models such as the multinomial and Dirichlet-multinomial distributions, which may impose a correlation structure not suitable for microbiome data.ObjectiveTo develop a methodology that accounts for compositional constraints to reduce false discoveries in detecting differentially abundant taxa at an ecosystem level, while maintaining high statistical power.MethodsWe introduced a novel statistical framework called analysis of composition of microbiomes (ANCOM). ANCOM accounts for the underlying structure in the data and can be used for comparing the composition of microbiomes in two or more populations. ANCOM makes no distributional assumptions and can be implemented in a linear model framework to adjust for covariates as well as model longitudinal data. ANCOM also scales well to compare samples involving thousands of taxa.ResultsWe compared the performance of ANCOM to the standard t-test and a recently published methodology called Zero Inflated Gaussian (ZIG) methodology (1) for drawing inferences on the mean taxa abundance in two or more populations. ANCOM controlled the false discovery rate (FDR) at the desired nominal level while also improving power, whereas the t-test and ZIG had inflated FDRs, in some instances as high as 68% for the t-test and 60% for ZIG. We illustrate the performance of ANCOM using two publicly available microbial datasets in the human gut, demonstrating its general applicability to testing hypotheses about compositional differences in microbial communities.ConclusionAccounting for compositionality using log-ratio analysis results in significantly improved inference in microbiota survey data.
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