VEGAN, a package of R functions for community ecology

Dixon, Philip M.

doi:10.1111/j.1654-1103.2003.tb02228.x

Cited by 4,850 publications

(3,317 citation statements)

References 3 publications

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“…Effects of time and treatment were evaluated by two-way analysis of variance (ANOVA) (variables "time" and "treatment") and the Bonferroni post hoc test. In case of non-normally distributed data, these were analyzed using the nonparametric "adonis" Permutational Multivariate Analysis of Variance using distance matrices (Anderson 2001) of the R software package "vegan" (Dixon 2003;Oksanen et al 2011), R statistic software version 2.13.1.…”

Section: Resultsmentioning

confidence: 99%

Age-dependent expression of stress and antimicrobial genes in the hemocytes and siphon tissue of the Antarctic bivalve, Laternula elliptica, exposed to injury and starvation

Husmann

Abele

Rosenstiel

et al. 2014

Cell Stress and Chaperones

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Increasing temperatures and glacier melting at the Western Antarctic Peninsula (WAP) are causing rapid changes in shallow coastal and shelf systems. Climate change-related rising water temperatures, enhanced ice scouring, as well as coastal sediment runoff, in combination with changing feeding conditions and microbial community composition, will affect all elements of the nearshore benthic ecosystem, a major component of which is the Antarctic soft-shelled clam Laternula elliptica. A 454-based RNA sequencing was carried out on tissues and hemocytes of L. elliptica, resulting in 42,525 contigs, of which 48 % was assigned putative functions. Changes in the expression of putative stress response genes were then investigated in hemocytes and siphon tissue of young and old animals subjected to starvation and injury experiments in order to investigate their response to sedimentation (food dilution and starvation) and iceberg scouring (injury). Analysis of antioxidant defense (Le-SOD and Lecatalase), wound repair (Le-TIMP and Le-chitinase), and stress and immune response (Le-HSP70, Le-actin, and Letheromacin) genes revealed that most transcripts were more clearly affected by injury rather than starvation. The upregulation of these genes was particularly high in the hemocytes of young, fed individuals after acute injury. Only minor changes in expression were detected in young animals under the selected starvation conditions and in older individuals. The stress response of L. elliptica thus depends on the nature of the environmental cue and on age. This has consequences for future population predictions as the environmental changes at the WAP will differentially impact L. elliptica age classes and is bound to alter population structure.

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Section: Resultsmentioning

confidence: 99%

Age-dependent expression of stress and antimicrobial genes in the hemocytes and siphon tissue of the Antarctic bivalve, Laternula elliptica, exposed to injury and starvation

Husmann

Abele

Rosenstiel

et al. 2014

Cell Stress and Chaperones

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“…Community structure was analyzed in R with phyloseq (McMurdie and Holmes, 2013) and plotted with ggplot2 (Wickham, 2009). Analysis of similarities (ANOSIM) was performed in R using VEGAN v.2.0-8 (Dixon, 2003).…”

Section: S Illumina Tag Sequencingmentioning

confidence: 99%

Microbiome shifts and the inhibition of quorum sensing by Black Band Disease cyanobacteria

et al. 2015

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Disruption of the microbiome often correlates with the appearance of disease symptoms in metaorganisms such as corals. In Black Band Disease (BBD), a polymicrobial disease consortium dominated by the filamentous cyanobacterium Roseofilum reptotaenium displaces members of the epibiotic microbiome. We examined both normal surface microbiomes and BBD consortia on Caribbean corals and found that the microbiomes of healthy corals were dominated by Gammaproteobacteria, in particular Halomonas spp., and were remarkably stable across spatial and temporal scales. In contrast, the microbial community structure in black band consortia was more variable and more diverse. Nevertheless, deep sequencing revealed that members of the disease consortium were present in every sampled surface microbiome of Montastraea, Orbicella and Pseudodiploria corals, regardless of the health status. Within the BBD consortium, we identified lyngbic acid, a cyanobacterial secondary metabolite. It strongly inhibited quorum sensing (QS) in the Vibrio harveyi QS reporters. The effects of lyngbic acid on the QS reporters depended on the presence of the CAI-1 receptor CqsS. Lyngbic acid inhibited luminescence in native coral Vibrio spp. that also possess the CAI-1-mediated QS. The effects of this naturally occurring QS inhibitor on bacterial regulatory networks potentially contribute to the structuring of the interactions within BBD consortia.

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“…Differences in community composition were tested using the non-parametric ANOSIM analysis (available in the VEGAN package of R; Dixon, 2003) on matrices of the unweighted Unifrac (Phylogenetic Diversity; Lozupone and Knight, 2005) and Jaccard (OTU diversity) distances. For each diversity index calculated, sample sizes were normalized by randomly selecting the number of sequences in the smallest sample from all other samples, computing the distance matrix, and then calculating the mean matrix values from 1000 such random samplings.…”

Section: Computing and Comparing Community Similaritymentioning

confidence: 99%

Coral-associated marine fungi form novel lineages and heterogeneous assemblages

Amend

Barshis²,

Oliver³

2011

The ISME Journal

141

100

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Coral stress tolerance is intricately tied to the animal's association with microbial symbionts. The most well-known of these symbioses is that between corals and their dinoflagellate photobionts (Symbiodinium spp.), whose genotype indirectly affects whether a coral can survive cyclical and anthropogenic warming events. Fungi comprise a lesser-known coral symbiotic community whose taxonomy, stability and function is largely un-examined. To assess how fungal communities inside a coral host correlate with water temperature and the genotype of co-occurring Symbiodinium, we sampled Acropora hyacinthus coral colonies from adjacent natural pools with different water temperatures and Symbiodinium identities. Phylogenetic analysis of coral-associated fungal ribosomal DNA amplicons showed a high diversity of Basidiomycetes and Ascomycetes, including several clades separated from known fungal taxa by long and well-supported branches. Community similarity did not correlate with any measured variables, and total fungal community composition was highly variable among A. hyacinthus coral colonies. Colonies in the warmer pool contained more phylogenetically diverse fungal communities than the colder pool and contained statistically significant 'indicator' species. Four taxa were present in all coral colonies sampled, and may represent obligate associates. Messenger RNA sequenced from a subset of these same colonies contained an abundance of transcripts involved in metabolism of complex biological molecules. Coincidence between the taxonomic diversity found in the DNA and RNA analysis indicates a metabolically active and diverse resident marine fungal community.

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VEGAN, a package of R functions for community ecology

Cited by 4,850 publications

References 3 publications

Age-dependent expression of stress and antimicrobial genes in the hemocytes and siphon tissue of the Antarctic bivalve, Laternula elliptica, exposed to injury and starvation

Age-dependent expression of stress and antimicrobial genes in the hemocytes and siphon tissue of the Antarctic bivalve, Laternula elliptica, exposed to injury and starvation

Microbiome shifts and the inhibition of quorum sensing by Black Band Disease cyanobacteria

Coral-associated marine fungi form novel lineages and heterogeneous assemblages

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