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Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification.

ABSTRACT: BACKGROUND:Next-generation-sequencing (NGS) technologies combined with a classic DNA barcoding approach have enabled fast and credible measurement for biodiversity of mixed environmental samples. However, the PCR amplification involved in nearly all existing NGS protocols inevitably introduces taxonomic biases. In the present study, we developed new Illumina pipelines without PCR amplifications to analyze terrestrial arthropod communities. RESULTS:Mitochondrial enrichment directly followed by Illumina shotgun sequencing, at an ultra-high sequence volume, enabled the recovery of Cytochrome c Oxidase subunit 1 (COI) barcode sequences, which allowed for the estimation of species composition at high fidelity for a terrestrial insect community. With 15.5 Gbp Illumina data, approximately 97% and 92% were detected out of the 37 input Operational Taxonomic Units (OTUs), whether the reference barcode library was used or not, respectively, while only 1 novel OTU was found for the latter. Additionally, relatively strong correlation between the sequencing volume and the total biomass was observed for species from the bulk sample, suggesting a potential solution to reveal relative abundance. CONCLUSIONS:The ability of the new Illumina PCR-free pipeline for DNA metabarcoding to detect small arthropod specimens and its tendency to avoid most, if not all, false positives suggests its great potential in biodiversity-related surveillance, such as in biomonitoring programs. However, further improvement for mitochondrial enrichment is likely needed for the application of the new pipeline in analyzing arthropod communities at higher diversity.

SUBMITTER: Zhou X

PROVIDER: S-EPMC3637469 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification.

Zhou Xin X Li Yiyuan Y Liu Shanlin S Yang Qing Q Su Xu X Zhou Lili L Tang Min M Fu Ribei R Li Jiguang J Huang Quanfei Q

GigaScience 20130327 1

<h4>Background</h4>Next-generation-sequencing (NGS) technologies combined with a classic DNA barcoding approach have enabled fast and credible measurement for biodiversity of mixed environmental samples. However, the PCR amplification involved in nearly all existing NGS protocols inevitably introduces taxonomic biases. In the present study, we developed new Illumina pipelines without PCR amplifications to analyze terrestrial arthropod communities.<h4>Results</h4>Mitochondrial enrichment directly ...[more]

PMID: 23587339

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Project description:Reefs formed by Ostrea edulis, the European native oyster, are among many biogenic habitats that have declined globally. European oyster habitats are now rare, and undisturbed examples have not been described. As more is understood of the ecosystem services provided by the reefs, oyster restoration efforts are on the rise, becoming a more prominent component of Europe's portfolio of marine conservation practices. It is therefore important to establish the relationship between the development of oyster reefs and their associated biotic community if the biodiversity benefits are to be accurately predicted and the progress of restoration projects assessed. The Loch Ryan oyster fishery in Southwest Scotland is the last of its type and uses a rotational harvest system where different areas are fished each year and then left for six years before they are fished again. This provided an opportunity to study the effect of oyster reef development and biodiversity gain at different stages of habitat recovery. In this study three treatments were surveyed for faunal biodiversity, oyster shell density and oyster shell percentage cover. Treatments were plots that had been harvested one year before, two years before, and six years before the study. The treatments were surveyed with SCUBA using a combination of video transects and photo quadrats. Oyster shell density, oyster shell percent cover and macrofaunal biodiversity differed significantly between treatments, with the highest values observed in the six-year treatment. Shell density was 8.5 times higher in the six-year treatment compared to the one-year treatment, whilst Shannon-Wiener's diversity was 60.5% higher, and Margalef's richness 68.8% higher. Shell density and percent cover had a significant positive relationship with macrofaunal biodiversity. This is probably due to the provision of increased structural complexity in the matrix of live and dead oyster shells. Projecting forward the trend of biodiversity increase in relation to time since disturbance indicates that full recovery would take approximately ten years in which time diversity (Shannon-Wiener) would probably have doubled. The findings from the present study indicate the probable biodiversity benefits of oyster habitat restoration and a cost-effective metric (shell density) to judge progress in restoration projects.

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Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification.

Publications

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification.

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