The conventional analysis of zooplankton samples is by sorting, identifying and counting the plankton using a low magnification stereomicroscope. For species-level identification a higher magnification conventional microscope is often needed to distinguish the tiny morphological details between species. See the resources page for sources to use in plankton identification.
Morphological identification allows for species-level identification in many taxa. Morphological identification of plankton samples is done by specialists experienced in taxonomy; the identification of organisms. Depending on the diversity and density of organisms in a sample a specialist needs hours to days to analyse a sample. This makes analysing plankton samples time consuming and expensive and has unfortunately lead to a lack of monitoring of zooplankton in many areas.
Novel techniques for plankton sampling
Recent technological advancements have made it possible to to sample and analyse plankton at high spatial, temporal and/or taxonomical resolution.
For this technique DNA from a mixed sample is extracted, sequenced and compared with a database of known DNA sequences for species to find out which species’ DNA was present in the samples. This allows for efficient and quick identification of many species, even ones that cannot be distinguished from other species by conventional means such as cryptic species and larval stages of many invertebrates. Estimating the abundance of organisms using DNA-based methods is still challenging but the accuracy of abundance estimates will likely increase with improvements in methodology. An important caveat with DNA metabarcoding is that in order to detect a species in a sample its DNA sequence data for the targeted gene region should be available. This means that it is important to have a complete well and curated reference database of barcodes.
In Plankton Imaging, images of planktonic organisms are collected, stored and classified. Advantages in camera technology, data storage and computer vision are enabling the acquisition, storage and processing of large volumes of images. Many different options are available to image plankton samples in the lab and directly in the water!
Imaging of plankton samples
Analysis of plankton samples using imaging can be done with different approaches. In flow-through systems a sample is pumped through a small transparent flow cell where a camera images each particle as it passes by. Commercially available flow through systems are available such as the FlowCam and for smaller plankton imaging flow cytometers such as the cytosense and imaging flow cytobot. There is also a great initiative to develop a low-cost open source option for flow through systems, the PlanktoScope.
An alternative approach is to scan samples using a flatbed scanner (such as the zooscan) where a sample is poured on a glass plate and scanned in the same way as you would scan a document. Using computer vision techniques individuel particles are identified on the images and classified. For the classification researchers developed an online tool called EcoTaxa where you can upload your dataset and even use data collected by others to train a classifier to classify the objects on your images. Alternatively you can develop your own analysis pipeline.
In-situ plankton imaging
With in-situ plankton imaging you image plankton directly in its natural environment. This can be done using underwater microscopes mounted on frames that are deployed from ships, or by pumping water from outside of a ship through an onboard flow cell with a camera system. In this way you can examine plankton at a high spatial and temporal resolution without having to take thousands of samples! This saves researchers a lot of time and money, and no animals need to be killed for it. Combining high resolution plankton imaging with simultaneous measurements of environmental parameters like temperature, salinity, depth and oxygen concentration allows investigation of plankton dynamics at fine scales impossible to achieve using traditional net sampling.
In-situ plankton imaging systems are generally optimised to sample a certain size range of organisms. Some examples of in-situ imaging systems are the ISIIS, CPICS, VPR and UVP . The Plankton Imager is a system that is used onboard research vessels.