Microscopy versus automated imaging flow cytometry for detecting and identifying rare zooplankton

Stanislawczyk, Keara; Johansson, Mattias L.; MacIsaac, Hugh J.

doi:10.1007/s10750-017-3382-1

Cited by 10 publications

(7 citation statements)

References 27 publications

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“…For example, the focus of the national Undaria pinnatifida strategy in New Zealand is to prevent human-mediated transfer of the kelp to offshore islands of high conservation value that are suitable for establishment but beyond its natural dispersal capacity (Forrest et al, 2009 , 2015), are needed for these activities to reduce the potential of transferring unwanted NIS into Arctic waters (Minchin, 2007 horizon scanning is conducted to systematically evaluate potential threats and opportunities in order to guide research, policy, and management responses (Ricciardi et al, 2017;Sutherland & Woodroof, 2009). This process may involve literature review, interviews, expert workshops, Delphi questionnaires, expert consultation, trend analysis, and/or risk assessment (Ricciardi et al, 2017;Roy, et al, 2014;Sutherland & Woodroof, 2009 However, NIS may be overlooked if they are rare or morphologically cryptic, and sampling methods can result in false negatives (i.e., failure to detect the occurrence of NIS in a given environment) at the initial stage of an invasion (Delaney & Leung, 2010;Stanislawczyk, Johansson, & MacIsaac, 2018). We recommend the use of molecular techniques to aid in early detection of NIS (Chown et al, 2015;Darling & Frederick, 2018;Ricciardi et al, 2017).…”

Section: Recommen Dationsmentioning

confidence: 99%

“…Horizon scanning may also be used as a tool to screen NIS currently absent in certain Arctic LMEs, but present in neighboring regions or other regions that are connected via established pathways including shipping, aquaculture activities, live food trade, and wild fisheries. This example also highlights the need to coordinate NIS management strategies among Arctic nations, as introduced species may unintentionally spread to neighboring countries.Early detection of undesired NIS at potential high-risk regions, such as the Iceland Shelf, the Norwegian Sea, and the Barents Sea, is essential for protecting the Arctic region from new invasions.However, NIS may be overlooked if they are rare or morphologically cryptic, and sampling methods can result in false negatives (i.e., failure to detect the occurrence of NIS in a given environment) at the initial stage of an invasion(Delaney & Leung, 2010;Stanislawczyk, Johansson, & MacIsaac, 2018). The Red King Crab was introduced into the Barents Sea in the 1960s to establish a commercial fishery(Dvoretsky & Dvoretsky, 2015).…”

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confidence: 99%

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Climate change opens new frontiers for marine species in the Arctic: Current trends and future invasion risks

Chan

Stanislawczyk

Sneekes

et al. 2018

Global Change Biology

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148

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Climate change and increased anthropogenic activities are expected to elevate the potential of introducing nonindigenous species (NIS) into the Arctic. Yet, the knowledge base needed to identify gaps and priorities for NIS research and management is limited. Here, we reviewed primary introduction events to each ecoregion of the marine Arctic realm to identify temporal and spatial patterns, likely source regions of NIS, and the putative introduction pathways. We included 54 introduction events representing 34 unique NIS. The rate of NIS discovery ranged from zero to four species per year between 1960 and 2015. The Iceland Shelf had the greatest number of introduction events (n = 14), followed by the Barents Sea (n = 11), and the Norwegian Sea (n = 11). Sixteen of the 54 introduction records had no known origins. The majority of those with known source regions were attributed to the Northeast Atlantic and the Northwest Pacific, 19 and 14 records, respectively. Some introduction events were attributed to multiple possible pathways. For these introductions, vessels transferred the greatest number of aquatic NIS (39%) to the Arctic, followed by natural spread (30%) and aquaculture activities (25%). Similar trends were found for introductions attributed to a single pathway. The phyla Arthropoda and Ochrophyta had the highest number of recorded introduction events, with 19 and 12 records, respectively. Recommendations including vector management, horizon scanning, early detection, rapid response, and a pan‐Arctic biodiversity inventory are considered in this paper. Our study provides a comprehensive record of primary introductions of NIS for marine environments in the circumpolar Arctic and identifies knowledge gaps and opportunities for NIS research and management. Ecosystems worldwide will face dramatic changes in the coming decades due to global change. Our findings contribute to the knowledge base needed to address two aspects of global change—invasive species and climate change.

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Section: Recommen Dationsmentioning

confidence: 99%

mentioning

confidence: 99%

Climate change opens new frontiers for marine species in the Arctic: Current trends and future invasion risks

Chan

Stanislawczyk

Sneekes

et al. 2018

Global Change Biology

Self Cite

148

View full text Add to dashboard Cite

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“…Light microscopy is still considered the golden standard technique providing high-resolution plankton images for qualitative and quantitative assessment. However, microscopy is a time-consuming approach that requires a high level of taxonomic skills and can result in human-based misclassification and underestimation of rare species 14 – 16 . Moreover, microscopy identification of plankton is limited by an increased sample variability and diversity of the spatial orientation of the plankton organisms in the imaging plane, presence of organic matter particles in the water samples, and decay.…”

Section: Introductionmentioning

confidence: 99%

Semi-automated classification of colonial Microcystis by FlowCAM imaging flow cytometry in mesocosm experiment reveals high heterogeneity during seasonal bloom

Mirasbekov

Zhumakhanova

Zhantuyakova

et al. 2021

Sci Rep

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A machine learning approach was employed to detect and quantify Microcystis colonial morphospecies using FlowCAM-based imaging flow cytometry. The system was trained and tested using samples from a long-term mesocosm experiment (LMWE, Central Jutland, Denmark). The statistical validation of the classification approaches was performed using Hellinger distances, Bray–Curtis dissimilarity, and Kullback–Leibler divergence. The semi-automatic classification based on well-balanced training sets from Microcystis seasonal bloom provided a high level of intergeneric accuracy (96–100%) but relatively low intrageneric accuracy (67–78%). Our results provide a proof-of-concept of how machine learning approaches can be applied to analyze the colonial microalgae. This approach allowed to evaluate Microcystis seasonal bloom in individual mesocosms with high level of temporal and spatial resolution. The observation that some Microcystis morphotypes completely disappeared and re-appeared along the mesocosm experiment timeline supports the hypothesis of the main transition pathways of colonial Microcystis morphoforms. We demonstrated that significant changes in the training sets with colonial images required for accurate classification of Microcystis spp. from time points differed by only two weeks due to Microcystis high phenotypic heterogeneity during the bloom. We conclude that automatic methods not only allow a performance level of human taxonomist, and thus be a valuable time-saving tool in the routine-like identification of colonial phytoplankton taxa, but also can be applied to increase temporal and spatial resolution of the study.

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“…Detection sensitivity-defined as the ability to detect a species at very low abundance-is directly related to sampling effort (Hoffman et al 2016, Stanislawczyk et al 2018. Intensive sampling can increase the probability of capturing an individual of a species present at low abundance.…”

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confidence: 99%

“…Intensive sampling can increase the probability of capturing an individual of a species present at low abundance. Sample processing methods may also affect detection sensitivity (Trebitz et al 2017, Stanislawczyk et al 2018. We explored effectiveness of 3 methods of sample analysis for zebra mussel detection, with a focus on veliger larvae.…”

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confidence: 99%

Detecting a spreading non-indigenous species using multiple methodologies

Johansson

Lavigne

Ramcharan

et al. 2020

Lake and Reservoir Management

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Non-indigenous species (NIS) are often introduced to novel environments at very low population abundance. Detecting the presence of such an NIS can be very challenging, particularly as it spreads from the initial establishment site. This provides an opportunity to test detection limits using different approaches. This study tested the detection capability of 3 methods as zebra mussels (Dreissena polymorpha) spread from south to north through Lake Winnipeg, Manitoba, Canada. Zebra mussel veliger larvae were detected using cross-polarized light microscopy (CPLM), flow cytometry and microscopy (FlowCam), and conventional polymerase chain reaction (cPCR) analysis of environmental DNA (eDNA) on the same samples. Abundance generally declined from south to north in the lake but was lowest at Calder's Dock (central). Although abundances could be quite low (i.e., <1 veliger/m 3 , Calder's Dock) CPLM prevalence-the percentage of samples with at least one veliger-was high throughout the lake (99-100% of samples). Prevalence was lower for cPCR and FlowCam but was statistically associated with veliger abundance. Using standardized 3 mL subsamples (0.06-0.18 m 3 of lake water sampled), all 3 methods had a high probability of veliger detection if large numbers of samples were processed. FlowCam was the most expensive method to process these 3 mL subsamples, while cPCR was least expensive and fastest. eDNA combined with intensive sampling is the most practical method for wide-scale monitoring programs for early detection. However, all 3 methods are complementary and could be deployed sequentially, with rapid initial sample processing using PCR, confirmation and density estimation with FlowCam, and detailed veliger counts using CPLM.

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Microscopy versus automated imaging flow cytometry for detecting and identifying rare zooplankton

Cited by 10 publications

References 27 publications

Climate change opens new frontiers for marine species in the Arctic: Current trends and future invasion risks

Climate change opens new frontiers for marine species in the Arctic: Current trends and future invasion risks

Semi-automated classification of colonial Microcystis by FlowCAM imaging flow cytometry in mesocosm experiment reveals high heterogeneity during seasonal bloom

Detecting a spreading non-indigenous species using multiple methodologies

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