Bioinformatics for Biomonitoring: Species Detection and Diversity Estimates Across Next-Generation Sequencing Platforms

Eckert, Isaac M.K.; Littlefair, Joanne E.; Zhang, Guang K.; Chain, Frédéric J. J.; Crease, Teresa J.; Cristescu, Melania E.

doi:10.1016/bs.aecr.2018.06.002

Cited by 5 publications

(6 citation statements)

References 64 publications

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“…The Illumina technology currently dominates the market (>65% of the studies analysed in this review), especially after the shutdown of the Roche 454 platform in 2013. Several studies found that sequence platform (Roche 454, Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5) did not affect species recovery (Braukmann et al., 2019 ; Eckert et al, 2018 ), although sequences obtained by Illumina had a higher quality (Braukmann et al., 2019 ). By contrast, a recent study by Singer, Fahner, Barnes, McCarthy, and Hajibabaei ( 2019 ) on eDNA metabarcoding of seawater found a much higher diversity in samples sequenced with the Illumina NovaSeq than with the MiSeq.…”

Section: Resultsmentioning

confidence: 99%

“…They recommend using a relaxed approach of restrictive PCR replicate filtering to find the optimal balance between additive filtering (leading to inflated diversity) and strict restrictive filtering (resulting in erroneously removed sequences). Torrent PGM and Ion Torrent S5) did not affect species recovery (Braukmann et al, 2019;Eckert et al, 2018), although sequences obtained by Illumina had a higher quality (Braukmann et al, 2019).…”

Section: Pcr Amplificationmentioning

confidence: 91%

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Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

2020

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Section: Resultsmentioning

confidence: 99%

Section: Pcr Amplificationmentioning

confidence: 91%

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

2020

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“…The Illumina technology currently dominates the market (>65% of the studies analyses in this review), especially after the shutdown of the Roche 454 platform in 2013. Several studies found that sequence platform (Roche 454, Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5) did not affect species recovery (Braukmann et al, 2019;Eckert et al, 2018), although sequences obtained by Illumina had a higher quality (Braukmann et al, 2019). On the contrary, a recent study by Singer et al (2019) on eDNA metabarcoding of seawater, found a much higher diversity in samples sequenced with the Illumina NovaSeq than with the MiSeq.…”

Section: 7sequencingmentioning

confidence: 99%

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

Loos

Nijland

2020

Preprint

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With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly implemented in ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, pre-processing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of 3 PCR replicates and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide-ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments, and the use of whole-genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments. Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

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“…Next-generation sequencing methods are commonly used molecular techniques to reveal the microbial composition of the biogas plants [16][17][18] as well as the seed sludge before the start-up of anaerobic digesters [9,19]. Rapid developments in the next-generation sequencing platforms enable greater sequencing depth and highresolution analyses [20] which provide deeper information about the community structure.…”

Section: Introductionmentioning

confidence: 99%

Comparative Assessment of Biogas Production Potential of the Most Abundant Agro-residues in Turkey

Özbayram¹,

İnce²

2021

Deu Muhendislik Fakultesi Fen Ve Muhendislik

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Recent energy policies promote energy generations from green resources to meet sustainability criteria. Since Turkey is one of the largest agricultural producers globally, it has great biogas production potential. This study aims to evaluate the biomethane yields of the most abundant agroresidues in Turkey and to assess their potentials for contribution to biogas production. Within this scope, sunflower heads, tea residues, cotton stalks, and crop residues; wheat, rye, and triticale straws were collected from different regions of Turkey. Anaerobic batch digesters were conducted to investigate the biomethane production of the selected feedstock and operated for 30 days at 37°C. Each setup was conducted in triplicates and methane productions were monitored online. The main methane production route of the inoculum was determined as acetoclastic methanogenesis while Cloacimonetes, Firmicutes, and Bacteroidetes composed the core bacterial phyla. The greatest methane yield was observed in the digesters operated with the wheat straw followed (164 NmL/gVSinfluent) by triticale straw and sunflower head. The lowest yields were calculated for the digesters fed with the cotton stalks (71 NmL/gVSinfluent). To increase the biomethane potential yields in the anaerobic digesters operated with agro-residues and to make the anaerobic digesters more feasible, operational conditions should be optimized and physico-chemical and biological pre-treatment techniques and/or bioaugmentation applications should be integrated into the systems.

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Bioinformatics for Biomonitoring: Species Detection and Diversity Estimates Across Next-Generation Sequencing Platforms

Cited by 5 publications

References 64 publications

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

Comparative Assessment of Biogas Production Potential of the Most Abundant Agro-residues in Turkey

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