ampvis2: an R package to analyse and visualise 16S rRNA amplicon data

Andersen, Kasper Skytte; Kirkegaard, Rasmus Hansen; Karst, Soeren M.; Albertsen, Mads

doi:10.1101/299537

Cited by 494 publications

(385 citation statements)

References 11 publications

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“…Taxa bar plots were built using the plugin qiime taxa bar plot. The construction of heatmaps of amplicon sequence variant (ASV) relative abundances at order level were made using the R package "ampvis2" v. 2.4.6 (Andersen et al, 2018). The differences in taxa abundance at the phylum and genus level (between the rhizosphere and bulk soil samples at both sampling sites and between plant ages) were compared using Mann-Whitney U test using PAST version (2.17).…”

Section: Discussionmentioning

confidence: 99%

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

et al. 2020

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Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growthpromoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the Frontiers in Microbiology | www.frontiersin.org March 2020 | Volume 11 | Article 198 Garcia-Lemos et al.Under the Christmas Tree greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.

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Section: Discussionmentioning

confidence: 99%

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

et al. 2020

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“…Downstream analyses were conducted with the “phyloseq”, “vegan”, “ampvis2” and “ggplot2” R packages or custom R scripts (35)), ((36)), ((37)), ((38)), ((39). Samples with fewer than 1000 reads for 16S and 200 reads for ITS were excluded from the resulting table.…”

Section: Methodsmentioning

confidence: 99%

Higher stochasticity of microbiota composition in seedlings of domesticated wheat compared to wild wheat

Özkurt

Hassani

Sesiz

et al. 2019

Preprint

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26Plants constitute an ecological niche for microbial communities that colonize different 27 plant tissues and explore the plant habitat for reproduction and dispersal. The 28 association of microbiota and plant may be altered by ecological and evolutionary 29 changes in the host population. Seedborne microbiota, expected to be largely vertically-30 transferred, have the potential to co-adapt with their host over generations. Reduced 31 host diversity because of strong directional selection and polyploidization during plant 32 domestication and cultivation may have impacted the assembly and transmission of 33 seed-associated microbiota. Nonetheless, the effect of plant domestication on the 34 diversity of their associated microbes is poorly understood. Here we show that microbial 35 communities in domesticated wheat, Triticum aestivum, are less diverse but more 36 inconsistent among individual plants compared to the wild wheat species, T. 37 dicoccoides. We found that diversity of microbes in seeds overall is low, but comparable 38 in different wheat species, independent of their genetic and geographic origin. 39However, the diversity of seedborne microbiota that colonize the roots and leaves of 40 the young seedling is significantly reduced in domesticated wheat genotypes. Moreover, 41we observe a higher variability between replicates of T. aestivum suggesting a stronger 42 effect of chance events in microbial colonization and assembly. We also propagated wild 43 and domesticated wheat in two different soils and found that different factors govern 44 the assembly of soil-derived and seedborne microbial communities. Overall, our results 45 demonstrate that the role of stochastic processes in seedborne microbial community 46 assembly is larger in domesticated wheat compared to the wild wheat. We suggest that 47 the directional selection on the plant host and polyploidization events during 48 domestication may have decreased the degree of wheat-microbiota interactions and 49 consequently led to a decreased stable core microbiota. 50 51

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“…However, based on visual signs, including male chest stains, body size, behaviour, and the presence of an infant, we inferred the age of two males and one female to be above 4 years, while one female was estimated to be 3-4 years of age uchime_ref) mode against the PR 2 database (version 4.11.0) (Guillou et al 2013). The following steps were conducted with the package ampvis2 (version 2.3.19) (Skytte et al 2018) in R (version 3.4.4) (R Core Team 2018). We performed sample comparisons at the same surveying effort, using the lowest number of sequences by subsampling (2600 reads per sample).…”

Section: Parasite Analysesmentioning

confidence: 99%

One size fits all? Relationships among group size, health, and ecology indicate a lack of an optimal group size in a wild lemur population

Rudolph

Fichtel

Schneider

et al. 2019

Behav Ecol Sociobiol

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Group size is a key component of sociality and can affect individual health and fitness. However, proximate links explaining this relationship remain poorly understood, partly because previous studies neglected potential confounding effects of ecological factors. Here, we correlated group size with various measures of health while controlling for measures of seasonality and habitat quality, to explore trade-offs related to group living in a mainly folivorous primate-Verreaux's sifakas (Propithecus verreauxi). Over a course of 2 years, we studied 42 individuals of 7 differently sized groups (range 2-10) and combined measures of faecal glucocorticoid metabolites (n > 2300 samples), parasitism (n > 500 samples), ranging and activity patterns, together with estimates of habitat quality (measures of~7000 feeding trees). None of our measures was correlated with group size, while seasonality, but not habitat quality, impacted almost all examined variables. We conclude that group size alone might be insufficient to explain patterns in the sociality-health nexus or that the small range of group sizes in this species does not induce effects suggested for species living in larger groups. An optimal group size balancing the advantages and disadvantages of living in differently sized groups may not exist for Verreaux's sifakas. Our results do not support predictions of the ecological constraints hypothesis or the optimal group size hypothesis as they may only account for species limited in group size by ecological factors-a condition that may not apply to the majority of folivorous mammals, which seem to be limited by social factors. Communicated by M. A. van NoordwijkSignificance statement Group size is a key component of group living and can crucially impact individual health. Ecological variables may modulate this relationship, but they were often neglected in previous studies. To better understand the links between sociality and health, we, for the first time in a mammal, simultaneously examined variation in ranging patterns, daily activities, glucocorticoid concentrations, and parasitism as a function of group size and under consideration of measures of seasonality and habitat quality in wild Verreaux's sifakas (Propithecus verreauxi). Group size had no impact on individual health indicators, while seasonal variation in food availability and temperature differences, but not habitat quality, affected the majority of variables. We demonstrate strong impacts of environmental factors on socio-ecological traits and conclude that group size on its own might be insufficient to explain patterns in the sociality-health nexus.

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ampvis2: an R package to analyse and visualise 16S rRNA amplicon data

Cited by 494 publications

References 11 publications

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development

Higher stochasticity of microbiota composition in seedlings of domesticated wheat compared to wild wheat

One size fits all? Relationships among group size, health, and ecology indicate a lack of an optimal group size in a wild lemur population

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