Early detection of invasive species in marine ecosystems using high-throughput sequencing: technical challenges and possible solutions

Xiong, Wei; Li, Haitao; Zhan, Aibin

doi:10.1007/s00227-016-2911-1

Cited by 56 publications

(41 citation statements)

References 71 publications

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“…Our results showed high congruence of geographical distribution patterns among different clustering scenarios ( p < 0.001), and the distinct variation between areas was consistently detected by each clustering methods (Table ), although both the OTU number and proportions of taxonomy in each clustering threshold were not unchanged, especially for clustering threshold of 99% (Figure S2 and Supporting Information Table S1), which had been emphasized by previous zooplankton studies (Xiong, Li, Zhan, et al., ; Zhan et al., ). Studies have showed that the sensibility of a high level identity threshold (e.g., 99%) might lead to the inflation of OTU numbers because of impacts of sequencing errors (Flynn et al., ; Hirai, Kuriyama, Ichikawa, Hidaka, & Tsuda, ; Razgour et al., ).…”

Section: Discussionsupporting

confidence: 77%

“…PCR programme included an initial denaturation step at 95°C for 5 min, followed by 25 amplification cycles of 95°C for 30 s, 50°C for 30 s, 72°C for 90 s and a final elongation step at 72°C for 10 min. PCRs were performed in eight replicates for each sample to reduce biased sampling of rare taxa (Xiong, Li, & Zhan, ; Zhan & MacIsaac, ), and replicates for each sample were combined before purification (SanPrep Column PCR Product Purification Kit, Sangon Biotech, Shanghai, China). Subsequently, PCR products from 30 communities were pooled to form one library for sequencing.…”

Section: Methodsmentioning

confidence: 99%

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Testing clustering strategies for metabarcoding‐based investigation of community–environment interactions

Xiong

Zhan

2018

Molecular Ecology Resources

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The degradation of freshwater ecosystems has become a common ecological and environmental problem globally. Owing to the complexity of biological communities, there remain tremendous technical challenges for investigating influence of environmental stressors (e.g., chemical pollution) on biological communities. High-throughput sequencing-based metabarcoding provides a powerful tool to reveal complex interactions between environments and biological communities. Among many technical issues, the clustering strategies for operational taxonomic units (OTUs) which are crucial for assessing biodiversity of communities, may affect final conclusions. Here, we used zooplankton communities along an environmental pollution gradient in the Chaobai River in Northern China to test different clustering strategies, including nonclustering and clustering with varied thresholds. Our results showed that though the number of OTUs estimated by nonclustering strategies and clustering strategies with divergence thresholds of 99%-97% largely varied, they were able to identify the same set of significant environmental and spatial variables responsible for geographical distributions of zooplankton communities. In addition, the ecological conclusions obtained by clustering thresholds of 99%-97% were consistent with nonclustering strategies, where for all eight clustering scenarios we detected that species sorting predicted by environmental variables overrode dispersal as the dominant factor in structuring zooplankton communities. However, clustering with the divergence thresholds of <95% affected the environmental and spatial variables identified. We conclude that both newly developed nonclustering methods and traditional clustering methods with divergence thresholds ≥97% were reliable to reveal mechanisms of complex community-environment interactions, although different clustering strategies could lead to largely varied biodiversity estimates such as those for α-diversity.

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Section: Discussionsupporting

confidence: 77%

Section: Methodsmentioning

confidence: 99%

Testing clustering strategies for metabarcoding‐based investigation of community–environment interactions

Xiong

Zhan

2018

Molecular Ecology Resources

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“…To pool and sequence all 30 communities, we added unique 8‐nt nucleotide codes (also known as tags) to the 5′‐ends of both the forward and reverse primers for each zooplankton community (Parameswaran et al., ). PCRs were performed in eight replicates for each sample to reduce biased sampling of rare taxa (Xiong, Li, & Zhan, ; Zhan & MacIsaac, ). Each PCR mix (25 μl) consisted of approximately 100 ng of genomic DNA, 1 × PCR buffer, 2 m m of Mg 2+ , 0.2 m m of dNTP, 0.4 μ m of each primer and 2 U of Taq DNA polymerase (LA Taq , Takara Inc., Japan).…”

Section: Methodsmentioning

confidence: 99%

Zooplankton community structure along a pollution gradient at fine geographical scales in river ecosystems: The importance of species sorting over dispersal

Xiong

Chen

et al. 2017

Molecular Ecology

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The release of anthropogenic pollution into freshwater ecosystems has largely transformed biodiversity and its geographical distribution patterns globally. However, for many communities including ecologically crucial ones such as zooplankton, it is largely unknown how different communities respond to environmental pollution. Collectively, dispersal and species sorting are two competing processes in determining the structure and geographical distribution of zooplankton communities in running water ecosystems such as rivers. At fine geographical scales, dispersal is usually considered as the dominant factor; however, the relative role of species sorting has not been evaluated well, mainly because significant environmental gradients rarely exist along continuously flowing rivers. The Chaobai River in northern China represents a rare system, where a significant environmental gradient exists at fine scales. Here, we employed high-throughput sequencing to characterize complex zooplankton communities collected from the Chaobai River, and tested the relative roles of dispersal and species sorting in determining zooplankton community structure along the pollution gradient. Our results showed distinct patterns of zooplankton communities along the environmental gradient, and chemical pollutant-related factors such as total phosphorus and chlorophyll-a were identified as the major drivers for the observed patterns. Further partial redundancy analyses showed that species sorting overrode the effect of dispersal to shape local zooplankton community structure. Thus, our results reject the dispersal hypothesis and support the concept that species sorting caused by local pollution can largely determine the zooplankton community structure when significant environmental gradients exist at fine geographical scales in highly polluted running water ecosystems.

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“…Research in this field followed two different approaches, one focusing on the early detection of particular pest species (targeted or active surveillance; e.g., Ardura et al, 2015;Simpson et al, 2016), and the other involving monitoring of communities for signs of appearance of alien species (passive surveillance; e.g., Comtet et al, 2015;Zaiko et al, 2015;Abad et al, 2016;Brown et al, 2016;Xiong et al, 2016). Another side of invasion biology is the assessment of the impact of alien species on native assemblages.…”

Section: Introductionmentioning

confidence: 99%

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Wangensteen

Cebrián

Palacín

et al. 2018

Marine Pollution Bulletin

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Running title: community-wide effects of invasive algae in MPAs Highlights  Hard-bottom communities dominated by invasive algae were studied with metabarcoding  A size-fractionation method is developed for the metabarcoding of complex samples  A modified primer set is used for the amplification of a COI fragment  A semiquantitave abundance index is proposed for statistical analyses  Results show effects of canopy-forming invasive algae on the underlying communities AbstractWe analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.

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Early detection of invasive species in marine ecosystems using high-throughput sequencing: technical challenges and possible solutions

Cited by 56 publications

References 71 publications

Testing clustering strategies for metabarcoding‐based investigation of community–environment interactions

Testing clustering strategies for metabarcoding‐based investigation of community–environment interactions

Zooplankton community structure along a pollution gradient at fine geographical scales in river ecosystems: The importance of species sorting over dispersal

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

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