Early detection of eukaryotic communities from marine biofilm using high-throughput sequencing: an assessment of different sampling devices

Pochon, Xavier; Zaiko, Anastasija; Hopkins, Grant A.; Banks, Jonathan C.; Wood, Susanna A.

doi:10.1080/08927014.2015.1028923

Cited by 50 publications

(38 citation statements)

References 81 publications

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“…In marine environments, some metabarcoding studies have analysed ecological patterns looking for drivers of biodiversity (e.g., Dafforn et al, 2014; Fonseca et al, 2010; Fonseca et al, 2014; Chariton et al, 2015; Lallias et al, 2015; Brannock et al, 2016), while others have explored assessment of human impacts or early surveillance of introduced species (e.g., Bik et al, 2012b; Brannock et al, 2014; Pawlowski et al, 2014b; Lejzerowicz et al, 2015; Pochon et al, 2015; Zaiko et al, 2016). …”

Section: Introductionmentioning

confidence: 99%

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Guardiola

Wangensteen

Taberlet

et al. 2016

PeerJ

104

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We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts.

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Section: Introductionmentioning

confidence: 99%

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Guardiola

Wangensteen

Taberlet

et al. 2016

PeerJ

104

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“…The 454 pyrosequencing platform was used with increasing frequency prior to 2013 but declined in popularity after this date (e.g. Stoeck et al 2010;Pawlowski et al 2011;Yu et al 2012;Parducci et al 2013;Pochon et al 2013;Yang et al 2014;Zimmermann et al 2015), coinciding with a rise in the use of Illumina sequencing platforms for DNA analysis; however, the maximum number of studies using the latter system in any year was just seven (Costa et al 2015;Deiner et al 2015;Dong et al 2015;Ficotela et al 2015;Pansu et al 2015a;Pochon et al 2015b;Song et al 2015). The Ion Torrent platform was used just three times (all since 2013) among the 167 studies reviewed (Deagle et al 2013;Young et al 2014;Zaiko et al 2015).…”

Section: Summary Of Pcr Product Purification Approachesmentioning

confidence: 99%

“…DNA metabarcoding studies were uncommon across the continents of South America and Africa. Five studies were included from New Zealand Collins et al 2013;Pochon et al 2013Pochon et al , 2015bTeasdale et al 2013); however, a large number of other studies were not included in our search results including Hamdan et al (2011), Jangid et al (2013), Hug et al (2014), Koele et al (2014), Sharp et al (2014), Martinez-Garcia et al (2015) and Morrison-Whittle & Goddard (2015).…”

Section: Locations Of Prior Investigationsmentioning

confidence: 99%

“…The most commonly-adopted PCR purification approaches were the Agencourt AMPure XP system (e.g. Bazzicalupo et al 2013;Pochon et al 2015b;Song et al 2015), the Qiagen MinElute PCR purification kit (e.g. Stoeck et al 2010;Thomsen et al 2012a;Calvignac-Spencer et al 2013) and the Promega Wizard SV Gel and PCR Clean-Up system (e.g.…”

Section: Summary Of Pcr Product Purification Approachesmentioning

confidence: 99%

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Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

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Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

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“…Additional topics for future focus include: improving stake-holder collaboration (e.g. removing barriers to data sharing); implementing more rigorous biofouling-related data collection; addressing fundamental performance issues such as boundary layer hydrodynamics in relation to biofouling [71], and emerging molecular techniques for early-detection of non-native species [72]. • Do MRE devices/arrays act as artificial reefs?…”

Section: Gaps In Ecological Understandingmentioning

confidence: 99%

Setting an agenda for biofouling research for the marine renewable energy industry

Loxton

Macleod

Nall

et al. 2017

International Journal of Marine Energy

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Abstract:Extensive marine growth on man-made structures in the ocean is commonplace, yet there has been limited discussion about the potential implications of marine growth for the wave and tidal energy industry. In response, the Environmental Interactions of Marine Renewables (EIMR) Biofouling Expert Workshop was convened. Discussions involved participants from the marine renewable energy (MRE) industry, anti-fouling industry, academic institutions and regulatory bodies. The workshop aimed to consider both the benefits and negative effects of biofouling from engineering and ecological perspectives. In order to form an agenda for future research in the area of biofouling and the marine renewable energy industry, 119 topics were generated, categorised and prioritised. Identified areas for future focus fell within four overarching categories: operation and maintenance; structured design and engineering; ecology; and knowledge exchange. It is clear that understanding and minimising biofouling impacts on MRE infrastructure will be vital to the successful development of a reliable and cost effective MRE industry.

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Early detection of eukaryotic communities from marine biofilm using high-throughput sequencing: an assessment of different sampling devices

Cited by 50 publications

References 81 publications

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Setting an agenda for biofouling research for the marine renewable energy industry

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