The use of camera and video technologies for conducting underwater surveys has rapidly expanded over the past several decades. However, the utility of these systems can be significantly hampered by numerous logistical factors, including limited underwater visibility, rough bottom topography, and ease of use for the operator. Video studies can be difficult to compare when methods and terminologies differ. Here, we describe the development of a cost-effective diver-propelled underwater ski-based video system for rapidly acquiring videos in challenging shallow high-energy rocky benthic habitats for quantifying fish, macroalgae, and invertebrates in a coastal temperate system. The ski held the camera at a (relatively) fixed distance from the seafloor, we used parallel lasers to quantify our observations, and we used the standardized language and definitions in the Coastal and Marine Ecological Classification Standard (CMECS) to acquire consistent quantitative data to serve as an ecological baseline, also including archived images. Our results indicate that the ski proved to be an effective tool for capturing insightful data that would otherwise be very difficult and time consuming to collect. Our baseline and repeatable methods can be used by other investigators at this or other locations for monitoring, re-evaluation, or comparisons to other sites.

Microbes in the dark ocean are exposed to hydrostatic pressure increasing with depth. Activity rate measurements and biomass production of dark ocean microbes are, however, almost exclusively performed under atmospheric pressure conditions due to technical constraints of sampling equipment maintaining in situ pressure conditions. To evaluate the microbial activity under in situ hydrostatic pressure, we designed and thoroughly tested an in situ microbial incubator (ISMI). The ISMI allows autonomously collecting and incubating seawater at depth, injection of substrate and fixation of the samples after a preprogramed incubation time. The performance of the ISMI was tested in a high-pressure tank and in several field campaigns under ambient hydrostatic pressure by measuring prokaryotic bulk H-leucine incorporation rates. Overall, prokaryotic leucine incorporation rates were lower at in situ pressure conditions than under to depressurized conditions reaching only about 50% of the heterotrophic microbial activity measured under depressurized conditions in bathypelagic waters in the North Atlantic Ocean off the northwestern Iberian Peninsula. Our results show that the ISMI is a valuable tool to reliably determine the metabolic activity of deep-sea microbes at in situ hydrostatic pressure conditions. Hence, we advocate that deep-sea biogeochemical and microbial rate measurements should be performed under in situ pressure conditions to obtain a more realistic view on deep-sea biotic processes.

Because the diffusivity of particles undergoing the Brownian motion is inversely proportional to their sizes, the size distribution of submicron particles can be estimated by tracking their movement. This particle tracking analysis (PTA) has been applied in various fields, but mainly focused on resolving monodispersed particle populations and is rarely used for measuring oceanic particles that are naturally polydispersed. We demonstrated using Monte Carlo simulation that, in principle, PTA can be used to size natural, oceanic particles. We conducted a series of lab experiments using microbeads of NIST-traceable sizes to evaluate the performance of ViewSizer 3000, a PTA-based commercial instrument, and found two major uncertainties: (1) the sample volume varies with the size of particles and (2) the signal-to-noise ratio for particles of sizes < 200-250 nm was reduced and hence their concentration was underestimated with the presence of larger particles. After applying the volume correction, we found the instrument can resolve oceanic submicron particles of sizes greater than 250 nm with a mean absolute error of 3.9% in size and 38% in concentration.

Autonomous and cabled platforms are revolutionizing our understanding of ocean systems by providing 4D monitoring of the water column, thus going beyond the reach of ship-based surveys and increasing the depth of remotely sensed observations. However, very few commercially available sensors for such platforms are capable of monitoring large particulate matter (100-2000 m) and plankton despite their important roles in the biological carbon pump and as trophic links from phytoplankton to fish. Here, we provide details of a new, commercially available scientific camera-based particle counter, specifically designed to be deployed on autonomous and cabled platforms: the Underwater Vision Profiler 6 (UVP6). Indeed, the UVP6 camera-and-lighting and processing system, while small in size and requiring low power, provides data of quality comparable to that of previous much larger UVPs deployed from ships. We detail the UVP6 camera settings, its performance when acquiring data on aquatic particles and plankton, their quality control, analysis of its recordings, and streaming from in situ acquisition to users. In addition, we explain how the UVP6 has already been integrated into platforms such as BGC-Argo floats, gliders and long-term mooring systems (autonomous platforms). Finally, we use results from actual deployments to illustrate how UVP6 data can contribute to addressing longstanding questions in marine science, and also suggest new avenues that can be explored using UVP6-equipped autonomous platforms.

An ice buoy system was developed to measure oceanographic properties of freshwater plumes that occur in Arctic coastal oceans under landfast sea ice during the spring freshet. By implanting such systems into sea ice weeks or months in advance of the freshet event, sensors can be located immediately underneath the sea ice layer in situ at depths that riverine freshwater will occupy later when the freshet arrives. This observing approach is modular, can accommodate a wide range of sensors, is designed intentionally for use in remote regions, and can be readily deployed in any nearshore region that can be accessed by snowmachine. The buoy system incorporates an integral floatation collar that allows it to continue sampling as the coastal ocean becomes progressively ice free in the months after the freshet event. Automated sampling and telemetry via a satellite data network provide near-real-time observations of the timing and character of under-ice freshet plumes. An assessment study was done with an array of these ice buoy systems, outfitted with basic hydrographic and optical sensors and deployed in advance of the 2018 and 2019 freshets in landfast sea ice near the mouths of three coastal rivers in Stefansson Sound, Alaska.

Harmful algal blooms are increasing in duration and severity globally, resulting in increased research interest. The use of genetic sequencing technologies has provided a wealth of opportunity to advance knowledge, but also poses a risk to that knowledge if handled incorrectly. The vast numbers of sequence processing tools and protocols provide a method to test nearly every hypothesis, but each method has inherent strengths and weaknesses. Here, we tested six methods to classify and quantify metatranscriptomic activity from a harmful algal bloom dominated by spp. Three online tools were evaluated (Kaiju, MG-RAST, and GhostKOALA) in addition to three local tools that included a command line BLASTx approach, recruitment of reads to individual genomes, and recruitment to a combined composite genome generated from sequenced isolates with complete, closed genomes. Based on the analysis of each tool presented in this study, two recommendations are made that are dependent on the hypothesis to be tested. For researchers only interested in the function and physiology of spp., read recruitments to the composite genome, referred to as "Frankenstein's ", provided the highest total estimates of transcript expression. However, for researchers interested in the entire bloom microbiome, the online GhostKOALA annotation tool, followed by subsequent read recruitments, provided functional and taxonomic characterization, in addition to transcript expression estimates. This study highlights the critical need for careful evaluation of methods before data analysis.

Phytoplankton accessory pigments are commonly used to estimate phytoplankton size classes, particularly during development and validation of biogeochemical models and satellite ocean color-based algorithms. The diagnostic pigment analysis (DPA) is based on bulk measurements of pigment concentrations and relies on assumptions regarding the presence of specific pigments in different phytoplankton taxonomic groups. Three size classes are defined by the DPA: picoplankton, nanoplankton, and microplankton. Until now, the DPA has not been evaluated against an independent approach that provides phytoplankton size calculated on a per-cell basis. Automated quantitative cell imagery of microplankton and some nanoplankton, used in combination with conventional flow cytometry for enumeration of picoplankton and nanoplankton, provide a novel opportunity to perform an independent evaluation of the DPA. Here, we use a data set from the North Atlantic Ocean that encompasses all seasons and a wide range of chlorophyll concentrations (0.18-5.14 mg m). Results show that the DPA overestimates microplankton and picoplankton when compared to cytometry data, and subsequently underestimates the contribution of nanoplankton to total biomass. In contrast to the assumption made by the DPA that the microplankton size class is largely made up of diatoms and dinoflagellates, imaging-in-flow cytometry shows significant presence of diatoms and dinoflagellates in the nanoplankton size class. Additionally, chlorophyll  is commonly attributed solely to picoplankton by the DPA, but Chl -containing phytoplankton are observed with imaging in both nanoplankton and microplankton size classes. We suggest revisions to the DPA equations and application of uncertainties when calculating size classes from diagnostic pigments.

Holographic microscopy has emerged as a tool for in situ imaging of microscopic organisms and other particles in the marine environment: appealing because of the relatively larger sampling volume and simpler optical configuration compared to other imaging systems. However, its quantitative capabilities have so far remained uncertain, in part because hologram reconstruction and image recognition have required manual operation. Here, we assess the quantitative skill of our automated hologram processing pipeline (CCV Pipeline), to evaluate the size and concentration measurements of environmental and cultured assemblages of marine plankton particles, and microspheres. Over 1 million particles, ranging from 10 to 200 m in equivalent spherical diameter, imaged by the 4-Deep HoloSea digital inline holographic microscope (DIHM) are analyzed. These measurements were collected in parallel with a FlowCam (FC), Imaging FlowCytobot (IFCB), and manual microscope identification. Once corrections for particle location and nonuniform illumination were developed and applied, the DIHM showed an underestimate in ESD of about 3% to 10%, but successfully reproduced the size spectral slope from environmental samples, and the size distribution of cultures (, , and ) and microspheres. DIHM concentrations (order 1 to 1000 particles ml) showed a linear agreement ( = 0.73) with the other instruments, but individual comparisons at times had large uncertainty. Overall, we found the DIHM and the CCV Pipeline required extensive manual correction, but once corrected, provided concentration and size estimates comparable to the other imaging systems assessed in this study. Holographic cameras are mechanically simple, autonomous, can operate at very high pressures, and provide a larger sampling volume than comparable lens-based tools. Thus, we anticipate that these characterization efforts will be rewarded with novel discovery in new oceanic environments.

Inconsistency in taxonomic identification and analyst bias impede the effective use of diatom data in regional and national stream and lake surveys. In this study, we evaluated the effect of existing protocols and a revised protocol on the precision of diatom species counts. The revised protocol adjusts five elements of sample preparation, taxon identification and enumeration, and quality control (QC) samples. We used six independent datasets to assess the effect of the adjustments on analytical outcomes. The first dataset was produced by five analysts from three laboratories following a standard protocol (Charles et al. 2002). The remaining datasets were produced by 2-3 analysts in 1-3 laboratories following a revised protocol. The revised protocol included the following modifications: 1) use of Battarbee settling chambers to prepare coverslips, 2) development of coordinated pre-count voucher floras based on morphological operational taxonomic units (mOTUs), 3) random assignment of samples to analysts, 4) post-count identification and documentation of taxa, and 5) increased QC samples. The revised protocol reduced taxonomic bias, as measured by reduction in analyst signal, and improved similarity among QC samples. Reduced taxonomic bias improves the performance of biological assessments, facilitates transparency across studies, and refines estimates of diatom species distributions.

Chlorophyll fluorometry is one of the most commonly implemented approaches for estimating phytoplankton biomass in situ, despite documented sources of natural variability and instrumental uncertainty in the relationship between in vivo fluorescence and chlorophyll concentration. A number of strategies are employed to minimize errors and quantify natural variability in this relationship in the open ocean. However, the assumptions underlying these approaches are unsupported in coastal waters due to the short temporal and small spatial scales of variability, as well as the optical complexity. The largest source of variability in the in situ chlorophyll fluorometric signal is nonphotochemical quenching (NPQ). Typically, unquenched nighttime observations are interpolated over the quenched daytime interval, but this assumes a spatial homogeneity not found in tidally impacted coastal waters. Here, we present a model that provides a tidally resolved correction for NPQ in moored chlorophyll fluorescence measurements. The output of the model is a time series of unquenched chlorophyll fluorescence in tidal endmembers (high and low tide extremes), and thus a time series of phytoplankton biomass growth and loss in these endmember populations. Comparison between modeled and measured unquenched time series yields quantification of nonconservative variations in phytoplankton biomass. Tidally modeled interpolation between these endmember time series yields a highly resolved time series of unquenched daytime chlorophyll fluorescence values at the location of the moored sensor. Such data sets provide a critical opportunity for validating the satellite remotely sensed ocean color chlorophyll concentration data product in coastal waters.

Headwater streams are important in the carbon cycle and there is a need to better parametrize and quantify exchange of carbon-relevant gases. Thus, we characterized variability in the gas exchange coefficient ( ) and dissolved oxygen (O) gas transfer velocity () in two lowland headwaters of the River Avon (UK). The traditional one-station open-water method was complemented by in situ quantification of riverine sources and sinks of O (i.e., groundwater inflow, photosynthesis, and respiration in both the water column and benthic compartment) enabling direct hourly estimates of at the reach-scale (~ 150 m) without relying on the nighttime regression method. Obtained values ranged from 0.001 h to 0.600 h. Average daytime were a factor two higher than values at night, likely due to diel changes in water temperature and wind. Temperature contributed up to 46% of the variability in on an hourly scale, but clustering temperature incrementally strengthened the statistical relationship. Our analysis suggested that variability is aligned with dominant temperature trends rather than with short-term changes. Similarly, wind correlation with increased when clustering wind speeds in increments correspondent with dominant variations (1 m s). Time scale is thus an important consideration when resolving physical drivers of gas exchange. Mean estimates of from recent parametrizations proposed for upscaling, when applied to the settings of this study, were found to be in agreement with our independent O budget assessment (within < 10%), adding further support to the validity of upscaling efforts aiming at quantifying large-scale riverine gas emissions.

Particulate organic carbon (POC) represents a small portion of total carbon in the ocean. However, it plays a large role in the turnover of organic matter through the biological pump and other processes. Early on since the development of the POC measurement technique in the 1960s, it was known that dissolved organic carbon (DOC) adsorbs and is retained both on and in the filter. That retained DOC is measured as if it was part of the particulate fraction, an artifact that can cause significant overestimates of POC concentration. We set out to address the long-standing question of whether the magnitude of the DOC adsorption is affected by the quantity and quality of the dissolved organic matter in the sample. However, our results precluded an unequivocal answer to that question; nevertheless, the experimental data generated did allow us to develop and test predictive models that relate the mass of carbon adsorbed to the volume of sample filtered. The results indicate that the uptake of DOC can be predicted using an exponential model and that a saturation point is approached when approximately a half-liter of water is filtered. This model can be a valuable tool for correcting existing POC data sets that did not account for DOC adsorption. Nonetheless, this approach should not be regarded as a substitute for collecting in situ filter blanks in parallel with POC samples to prop-erly correct for this artifact.

Zooplankton dominate the abundance and biomass of multicellular animals in pelagic marine environments; however, traditional methods to characterize zooplankton communities are invasive and laborious. This study compares zooplankton taxonomic composition revealed through metabarcoding of the cytochrome oxidase I (COI) and 18S rRNA genes to traditional morphological identification by microscopy. Triplicates of three different sample types were collected from three coral reef sites in the Florida Keys National Marine Sanctuary: (1) 1 L surface seawater samples prefiltered through 3 m filters and subsequently collected on 0.22 m filters for eDNA (PF-eDNA); (2) 1 L surface seawater samples filtered on 0.22 m pore-size filters (environmental DNA; eDNA), and (3) zooplankton tissue samples from 64 m, 200 m, and 500 m mesh size net tows. The zooplankton tissue samples were split, with half identified morphologically and tissue DNA (T-DNA) extracted from the other half. The COI and 18S rRNA gene metabarcoding of PF-eDNA, eDNA, and T-DNA samples was performed using Illumina MiSeq. Of the families detected with COI and 18S rRNA gene metabarcoding, 40% and 32%, respectively, were also identified through morphological assessments. Significant differences in taxonomic composition were observed between PF-DNA, eDNA, and T-DNA with both genetic markers. PF-eDNA resulted in detection of fewer taxa than the other two sample types; thus, prefiltering is not recommended. All dominant copepod taxa (> 5% of total abundance) were detected with eDNA, T-DNA, and morphological assessments, demonstrating that eDNA metabarcoding is a promising technique for future biodiversity assessments of pelagic zooplankton in marine systems.

We developed an effective fluorometric technique to quantify extracellular carbonic anhydrase (eCA) present in natural seawater samples. The technique includes the separation of eCA from cells to achieve low detection limits through high signal : noise ratios. eCA was efficiently extracted from cell membranes by treatment with 0.1 M phosphate buffer containing 2.5 M NaCl. The free eCA specifically forms a fluorescent complex with dansylamide, and the detection limit of the complex is below 0.1 nM. We applied the technique to samples from different culture solutions and natural seawater collected from the Baltic Sea. We observed eCA concentrations to be in the range of 0.10-0.67 nM in natural seawater. The data indicated that this technique is very sensitive, accurate, and feasible for routine and shipboard measurement of eCA from natural seawater. It is therefore an effective and rapid tool to investigate the carbon acquisition of phytoplankton both in mono culture as well natural communities.

Coring is one of several standard procedures to extract sediments and their faunas from open marine, estuarine, and limnic environments. Achieving sufficiently deep penetration, obtaining large sediment volumes in single deployments, and avoiding sediment loss upon retrieval remain problematic. We developed a piston corer with a diameter of 16 cm that enables penetration down to 1.5 m in a broad range of soft bottom types, yields sufficient material for multiple analyses, and prevents sediment loss due to a specially designed hydraulic core catcher. A novel extrusion system enables very precise slicing and preserves the original sediment stratification by keeping the liners upright. The corer has moderate purchase costs and a robust and simple design that allows for a deployment from relatively small vessels as available at most marine science institutions. It can easily be operated by two to three researchers rather than by specially trained technicians. In the northern Adriatic Sea, the corer successfully extracted more than 50 cores from a range of fine mud to coarse sand, at water depths from three to 45 m. The initial evaluation of the cores demonstrated their usefulness for fauna sequences along with heavy metal, nutrient and pollutant analyses. Their length is particularly suited for historical ecological work requiring sedimentary and faunal sequences to reconstruct benthic communities over the last millennia.

This work assesses the components contributing to the combined uncertainty budget associated with the measurement of the Fe amount content by flow injection chemiluminescence (FI-CL) in <0.2 m filtered and acidified seawater samples. Amounts of loaded standard solutions and samples were determined gravimetrically by differential weighing. Up to 5% variations in the loaded masses were observed during measurements, in contradiction to the usual assumptions made when operating under constant loading time conditions. Hence signal intensities (V) were normalised to the loaded mass and plots of average normalised intensities (in V kg) vs. values of the Fe amount content (in nmol kg) added to a "low level" iron seawater matrix were used to produce the calibration graphs. The measurement procedure implemented and the uncertainty estimation process developed were validated from the agreement obtained with consensus values for three SAFe and GEOTRACES reference materials (D2, GS, and GD). Relative expanded uncertainties for peak height and peak area based results were estimated to be around 12% and 10% (coverage factor  = 2), respectively. The most important contributory factors were the uncertainty on the sensitivity coefficient (i.e., calibration slope) and the within-sequence-stability (i.e., the signal stability over several hours of operation; here 32 h). For GD, using peak height measurements, these factors contributed respectively 69.7% and 21.6% while the short-term repeatability accounted for only 7.9%. Therefore, an uncertainty estimation based on the intensity repeatability alone, as is often done in FI-CL studies, is not a realistic estimation of the overall uncertainty of the procedure.

Diatoms require silicic acid to construct ornately detailed cell walls called frustules. The growth and geographic distribution of diatoms is often controlled by the availability of silicic acid. Analytical methods exist to assess diatom community biogenic silica (bSiO) production, but partitioning production among taxa has been largely qualitative. We present a method for the quantitative analysis of taxa-specific silica production through labeling diatoms with the fluorescent dye PDMPO [2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole]. To make PDMPO a quantitative tool: diatom frustules were solubilized to assess the total diatom community incorporation by quantitation of PDMPO fluorescence using a fluorometer, and laser confocal microscopy was used to quantify the fluorescence of PDMPO in single diatom cells. We created a fluorescence standard to intercalibrate the raw fluorescence signals of the fluorometer and microscope and to determine the fluorescence per mole of PDMPO. PDMPO incorporation was converted to silica production using diatom bSiO:PDMPO incorporation ratios which varied systematically with silicic acid concentration. Above 3 μM Si(OH), bSiO:PDMPO was constant and PDMPO incorporation was converted to silica production using a mole ratio of 2,916 as determined from cultures. Below 3 μM, the ratio was a linear function of [Si(OH)] (bSiO:PDMPO = 912.6 × [Si(OH)]), as determined using data from two oceanographic cruises. Field evaluation of the method showed that total community PDMPO incorporation generally agreed to within 30% of radioisotope-determined silica production. This PDMPO method has the potential to be a powerful tool for understanding physiology, silicification and resource competition among diatom taxa.

Over the past four decades, mesocosm studies have been successfully used for a wide range of applications and have provided a lot of information on trophic interactions and biogeochemical cycling of aquatic ecosystem. However, the setup of such mesocosms (e.g., dimensions and duration of experiments) needs to be adapted to the relevant biological processes being investigated. Mixing of the water column is an important factor to be considered in mesocosm experiments because enclosing water in an artificial chamber always alters the mixing regime. Various approaches have been applied to generate mixing in experimental ecosystems, including pure mechanical mixing (e.g., using a disc), airlifts, bubbling with compressed air, and pumping. In this study, we tested different mixing techniques for outdoor mesocosms and their impact on plankton biomass and community composition. We compared mesocosms mixed with a disc, an airlift-system, and bubbling, and used a nonactively mixed mesocosm as a control. We investigated phytoplankton, ciliate, and zooplankton communities during a 19-d mesocosm experiment. Based on our results, we concluded that mechanical mixing with a disc was the most effective technique due to the undertow produced by lowering and lifting the disc. While no mixing technique affected seston biomass, zooplankton biomass was highest in the treatments mixed with the disc. The airlift treatments had the lowest relative share of small flagellates. However, no further differences in phytoplankton community composition occurred and no differences in zooplankton community composition existed between all actively mixed treatments.

Harmful algal blooms (HABs) are a serious public health risk in coastal waters. As the intensity and frequency of HABs continue to rise, new methods of detection are needed for reliable identification. Herein, we developed a high-throughput, multiplex, bead array technique for the detection of the dinoflagellates Karenia brevis and Karenia mikimotoi. The method combined the Luminex detection system with two novel technologies: locked nucleic acid-modified oligonucleotides (LNA) and Mirus Label IT(®) nucleic acid technology. To study the feasibility of the method, we evaluated the performance of modified and unmodified LNA probes with amplicon targets that were biotin labeled with two different strategies: direct chemical labeling (Mirus Label IT) versus enzymatic end-labeling (single biotinylated primer). The results illustrated that LNA probes hybridized to complementary single-stranded DNA with better affinity and displayed higher fluorescence intensities than unmodified oligonucleotide DNA probes. The latter effect was more pronounced when the assay was carried out at temperatures above 53°C degree. As opposed to the enzymatic 5' terminal labeling technique, the chemical-labeling method enhanced the level of fluorescence by as much as ~83%. The detection limits of the assay, which were established with LNA probes and Mirus Label IT system, ranged from 0.05 to 46 copies of rRNA. This high-throughput method, which represents the first molecular detection strategy to integrate Luminex technology with LNA probes and Mirus Label IT, can be adapted for the detection of other HABs and is well suited for the monitoring of red tides at pre-blooming and blooming conditions.

Studies using culture dependent methods have indicated that enterococci, the fecal indicator used to monitor marine waters for the potential of enteric disease risk to swimmers, can be abundant in beach sands and may contribute to water column indicator exceedances. A quantitative PCR (qPCR) method for the Enterococcus genus was tested and applied to more rapidly determine the amount of enterococci in beach sands and study their distribution over space and time. The qPCR method amplified a 23S rDNA sequence specific to Enterococcus (Ludwig and Schliefer, 2000), and was used to examine subsamples and composite samples of wet and dry beach sand from Avalon Bay, CA. The differences in efficiency of DNA recovery and inhibition in qPCR reactions were accounted for by spiking pairs of duplicate subsamples with a known amount of pGEM plasmid before or after extraction, respectively (Coyne et al. 2005). This study revealed levels of environmental inhibition that were similar in wet and dry sands, and efficiency of DNA recovery that was observably lower for wet beach sands and varied between years. Using the correction factors generated by this method to estimate the abundance of Enterococcus, we show that wet and dry beach sands both have Enterococcus spp. populations that can vary dramatically from day to day, and often are potentially higher than the equivalent health standards mandated for recreational waters.

Zooplankton organisms with short generation times, such as rotifers, are ideal models to study general ecological and evolutionary questions on the population level, because meaningful experiments can often be completed within a couple of weeks. Yet biological analysis of such populations is often extremely time consuming, owing to abundance estimation by counting, measuring body size, or determining the investment into sexual versus asexual reproduction. An automated system for sampling and analyzing experimental rotifer populations is described. It relies on image analysis of digital photographs taken from subsamples of the culture. The system works completely autonomously for up to several weeks and can sample up to 12 cultures at time intervals down to a few hours. It allows quantitative analysis of female population density at a precision equivalent to that of conventional methods (i.e., manual counts of samples fixed in Lugol solution), and it can also recognize males, which allows detecting temporal variation of sexual reproduction in such cultures. Another parameter that can be automatically measured with the image analysis system is female body size. This feature may be useful for studies of population productivity and/or in competition experiments with clones of different body size. In this article, I describe the basic setup of the system and tests on the efficiency of data collection, and show some example data sets on the population dynamics of different strains of the rotifer Brachionus calyciflorus.