Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

Chariton, Anthony A.; Court, Leon; Hartley, Diana; Colloff, Matthew J.; Hardy, Christopher M.

doi:10.1890/090115

Cited by 180 publications

(161 citation statements)

References 19 publications

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“…It appeared that kinorhynchs and macrofaunal diversity were sensitive to triclosan exposure; cnidarians, polychaetes, and meiofaunal diversity were sensitive to sedimentation effects; and nematodes, harpacticoids and their nauplii, macrofaunal bivalves, total abundance, and number of taxa were sensitive to both sedimentation and chemical exposure. In the case of kinorhyncha, there is a small but growing body of evidence suggesting that this phylum is sensitive to a range of environmental contaminants [23][24][25].…”

Section: Overall Changes In Benthic Communitiesmentioning

confidence: 99%

Use of a novel sediment exposure to determine the effects of triclosan on estuarine benthic communities

Chariton

Portis

et al. 2012

Enviro Toxic and Chemistry

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Abstract-Triclosan (5-chloro-2-[2,4-dichlorophenoxy]phenol) is a relatively new, commonly used antimicrobial compound found in many personal care products. Triclosan is toxic to marine organisms at the micrograms per liter level, can photodegrade to a dioxin, can accumulate in humans, and has been found to be stable in marine sediments for over 30 years. To determine the effects of triclosan on marine benthic communities, intact sediment cores were brought into the laboratory and held under flowing seawater conditions. A 2-cm layer of triclosan-spiked sediment was applied to the surface, and after a two-week exposure the meio-and macrofaunal communities were assessed for differences in composition relative to nonspiked cores. A high triclosan treatment (180 mg/kg dry wt) affected both the meio-and the macrobenthic communities. There were no discernible differences with a low-triclosan treatment (14 mg/kg dry wt). This exposure method is effective for testing the benthic community response to sediment contaminants, but improvements should be made with regard to the amount and method of applying the overlying sediment to prevent smothering of fragile benthic organisms. Environ.

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Section: Overall Changes In Benthic Communitiesmentioning

confidence: 99%

Use of a novel sediment exposure to determine the effects of triclosan on estuarine benthic communities

Chariton

Portis

et al. 2012

Enviro Toxic and Chemistry

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“…The alternative DNA-based tools have been developed and increasingly used for identification of bacteria, protists and fungi since two decades ago. More recently, the massively parallel DNA metabarcoding technology has been adopted for large-scale community-level identification of fungi (Jumpponen and Jones, 2009), protists (Chariton et al, 2010;Medinger et al, 2010) and animals (Porazinska et al, 2009). For meiofauna, metabarcoding studies have focussed on specific order to phylum-level groups such as nematodes or certain arthropods (Porazinska et al, 2009;Hajibabaei et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

et al. 2015

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Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.

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“…With developments in high-throughput sequencing technologies and bioinformatics pipelines, it is now possible to sequence a single genetic locus en masse from the environment and delimit species in large scale environmental (eDNA) metabarcoding surveys (2,3). Such eDNA surveys have been used to describe the diversity of microorganisms (4), macrofauna (5), fungi (6), and plants (7) in previously understudied habitats, such as the soil biota (8), sediments (9), and water (5,10). Faced with these technological advances, it is now more important than ever to evaluate the reliability of the genetic loci used for DNA taxonomy, and to assess the congruence of their results with morphological taxonomy.…”

mentioning

confidence: 99%

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

Tang

Leasi

Obertegger

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

309

287

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Molecular tools have revolutionized the exploration of biodiversity, especially in organisms for which traditional taxonomy is difficult, such as for microscopic animals (meiofauna). Environmental (eDNA) metabarcode surveys of DNA extracted from sediment samples are increasingly popular for surveying biodiversity. Most eDNA surveys use the nuclear gene-encoding smallsubunit rDNA gene (18S) as a marker; however, different markers and metrics used for delimiting species have not yet been evaluated against each other or against morphologically defined species (morphospecies). We assessed more than 12,000 meiofaunal sequences of 18S and of the main alternatively used marker [Cytochrome c oxidase subunit I (COI) mtDNA] belonging to 55 datasets covering three taxonomic ranks. Our results show that 18S reduced diversity estimates by a factor of 0.4 relative to morphospecies, whereas COI increased diversity estimates by a factor of 7.6. Moreover, estimates of species richness using COI were robust among three of four commonly used delimitation metrics, whereas estimates using 18S varied widely with the different metrics. We show that meiofaunal diversity has been greatly underestimated by 18S eDNA surveys and that the use of COI provides a better estimate of diversity. The suitability of COI is supported by cross-mating experiments in the literature and evolutionary analyses of discreteness in patterns of genetic variation. Furthermore its splitting of morphospecies is expected from documented levels of cryptic taxa in exemplar meiofauna. We recommend against using 18S as a marker for biodiversity surveys and suggest that use of COI for eDNA surveys could provide more accurate estimates of species richness in the future.DNA barcodes | species delimitation | microinvertebrates | environmental DNA

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Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA

Cited by 180 publications

References 19 publications

Use of a novel sediment exposure to determine the effects of triclosan on estuarine benthic communities

Use of a novel sediment exposure to determine the effects of triclosan on estuarine benthic communities

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna

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