Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

Visco, Joana Amorim; Apothéloz-Perret-Gentil, Laure; Cordonier, Arielle; Esling, Philippe; Pillet, Loïc; Pawłowski, Jan

doi:10.1021/es506158m

Cited by 173 publications

(148 citation statements)

References 46 publications

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“…Little is known about plastic-associated microbial eukaryotes in freshwaters, and there is a need for analyses targeting these organisms, not the least as they are known to occur on marine plastics [48,49]. Several advances have improved the suitability of metabarcoding for analyzing fungi, diatoms, and protists [85][86][87]. This approach is based on taxonomically informative markers and provides no direct information on metabolic activities.…”

Section: Analytical and Experimental Advances In Plastisphere Researchmentioning

confidence: 99%

Microplastic-Associated Biofilms: A Comparison of Freshwater and Marine Environments

Harrison

Hoellein

Sapp

et al. 2017

The Handbook of Environmental Chemistry

123

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Microplastics (<5 mm particles) occur within both engineered and natural freshwater ecosystems, including wastewater treatment plants, lakes, rivers, and estuaries. While a significant proportion of microplastic pollution is likely sequestered within freshwater environments, these habitats also constitute an important conduit of microscopic polymer particles to oceans worldwide. The quantity of aquatic microplastic waste is predicted to dramatically increase over the next decade, but the fate and biological implications of this pollution are still poorly understood. A growing body of research has aimed to characterize the formation, composition, and spatiotemporal distribution of microplastic-associated ("plastisphere") microbial biofilms. Plastisphere microorganisms have been suggested to play significant roles in pathogen transfer, modulation of particle buoyancy, and biodegradation of plastic polymers and co-contaminants, yet investigation of these topics within freshwater environments is at a very early stage. Here, what is known about marine plastisphere assemblages is systematically compared with up-to-date findings from freshwater habitats. Through analysis of key differences and likely commonalities between environments, we discuss how

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Section: Analytical and Experimental Advances In Plastisphere Researchmentioning

confidence: 99%

Microplastic-Associated Biofilms: A Comparison of Freshwater and Marine Environments

Harrison

Hoellein

Sapp

et al. 2017

The Handbook of Environmental Chemistry

123

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“…Initial studies inferring biotic indices from molecular data show the potential of metabarcoding for evaluating aquatic ecosystem quality Visco et al, 2015). However, before implementation of metabarcoding in regular biomonitoring programs, this approach needs to be benchmarked against morphological identification so that accurate taxonomic inferences and derived biotic indices can be ensured (Aylagas et al, 2014;Carugati et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

2016

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Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing (HTS) represents an alternative to rapidly, accurately, and cost-effectively analyze thousands of environmental samples simultaneously, and this method is increasingly used to characterize the metazoan taxonomic composition of a wide variety of environments. However, a comprehensive study benchmarking visual and metabarcoding-based taxonomic inferences that validates this technique for environmental monitoring is still lacking. Here, we compare taxonomic inferences of benthic macroinvertebrate samples of known taxonomic composition obtained using alternative metabarcoding protocols based on a combination of different DNA sources, barcodes of the mitochondrial cytochrome oxidase I gene and amplification conditions. Our results highlight the influence of the metabarcoding protocol in the obtained taxonomic composition and suggest the better performance of an alternative 313 bp length barcode to the traditionally 658 bp length one used for metazoan metabarcoding. Additionally, we show that a biotic index inferred from the list of macroinvertebrate taxa obtained using DNA-based taxonomic assignments is comparable to that inferred using morphological identification. Thus, our analyses prove metabarcoding valid for environmental status assessment and will contribute to accelerating the implementation of this technique to regular monitoring programs.

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“…Studies demonstrate DNA metabarcoding to be a reliable method for biodiversity assessment with potential for inferring biotic indices for marine ecosystem quality assessment (Aylagas et al, 2014;Pawlowski et al, 2014;Cowart et al, 2015;Elbrecht and Leese, 2015;Visco et al, 2015;Ferrera et al, 2016). Comparable results between molecular and traditional approaches are reported in a number of studies (Hirai et al, 2015a;Lejzerowicz et al, 2015;Aylagas et al, 2016Aylagas et al, , 2017Valentini et al, 2016), suggesting that assessment programs that require manually intensive sorting and visual inspection will be among the first to formally integrate molecular techniques.…”

Section: Applications Of Dna Sequencing To Marine Assessment Programsmentioning

confidence: 99%

DNA Sequencing as a Tool to Monitor Marine Ecological Status

et al. 2017

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Many ocean policies mandate integrated, ecosystem-based approaches to marine monitoring, driving a global need for efficient, low-cost bioindicators of marine ecological quality. Most traditional methods to assess biological quality rely on specialized expertise to provide visual identification of a limited set of specific taxonomic groups, a time-consuming process that can provide a narrow view of ecological status. In addition, microbial assemblages drive food webs but are not amenable to visual inspection and thus are largely excluded from detailed inventory. Molecular-based assessments of biodiversity and ecosystem function offer advantages over traditional methods and are increasingly being generated for a suite of taxa using a "microbes to mammals" or "barcodes to biomes" approach. Progress in these efforts coupled with continued improvements in high-throughput sequencing and bioinformatics pave the way for sequence data to be employed in formal integrated ecosystem evaluation, including food web assessments, as called for in the European Union Marine Strategy Framework Directive. DNA sequencing of bioindicators, both traditional (e.g., benthic macroinvertebrates, ichthyoplankton) and emerging (e.g., microbial assemblages, fish via eDNA), promises to improve assessment of marine biological quality by increasing the breadth, depth, and throughput of information and by reducing costs and reliance on specialized taxonomic expertise.

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Environmental Monitoring: Inferring the Diatom Index from Next-Generation Sequencing Data

Cited by 173 publications

References 46 publications

Microplastic-Associated Biofilms: A Comparison of Freshwater and Marine Environments

Microplastic-Associated Biofilms: A Comparison of Freshwater and Marine Environments

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

DNA Sequencing as a Tool to Monitor Marine Ecological Status

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