Collaborative Deep Learning Models to Handle Class Imbalance in FlowCam Plankton Imagery

Usingautomatedimagingtechnologies,itisnowpossibletogeneratepreviouslyunprecedented volumes of plankton image data which can be used to study the composition of plankton assemblages. However, the current need to manually classify individual images introduces a bottleneck into processing chains.AlthoughMachineLearningtechniqueshavebeenusedtotryandaddressthisissue,pasteffortshave suffered from accuracy limitations, especially in minority classes. Here we use state-of-the-art methods in Deep Learning to investigate suitable architectures for training an automated plankton classification system which achieves high efficacy for both abundant and rare taxa. We collected live plankton from Station L4 in the Western English Channel and imaged 11,371 particles covering 104 taxonomic groups using the automatedplanktonimagingsystemFlowCam.Theimagesetcontainedasevereclassimbalance,withsome taxa represented by > 600 images while other, rarer taxa were represented by just 14. We demonstrate that by allowing multiple Deep Learning models to collaborate in a single classification system, classification accuracyimprovesforminorityclasseswhencomparedwiththebestindividualmodel.Thetopcollaborative model achieved a 6 % improvement in F1 accuracy over the best individual model, while overall accuracy improved by 3.2 %. This resulted in a 97.4 % overall accuracy score and a 96.2 % F1 macro score on a separate holdout test set containing 104 taxonomic groups. Based on a survey of similar studies in the literature, we believe collaborative deep learning models can significantly improve the accuracy of existing automated plankton classification systems

Distribution, sedimentation and fate of pigment biomarkers following thermal stratification in the western Alboran Sea

A spring investigation of the phytoplankton in the western Alboran Sea (Mediterranean) was undertaken using chlorophyll and carotenoid biomarkers to characterize the community in the water column and in drifting sediment traps set at 100 and 200 m. During 2 drifter experiments, calm and sunny conditions induced a progressive thermal stratification that reduced pigment sedimentation into deeper water and confined the phytoplankton to the surface layer, resulting in an increase in chlorophyll biomass. 19'-Hexanoyloxyfucoxanthin (prymnesiophytes) and chlorophyll b (chlorophytes, prasinophytes, prochlorophytes) were the major accessory pigments, while fucoxanthin, alloxanthin and peridinin indicated the presence of diatoms, cryptophytes and dinoflagellates, respectively. The proportional contribution of each algal group to the chlorophyll a (chl a) biomass, as derived from multiple regression analysis, revealed that prymnesiophytes, cryptophytes and the green algal group collectively accounted for at least 75% in the upper 100 m, emphasizing the importance of the nanophytoplankton. Phaeopigments, dominated by phaeophorbide a2, were the main pigments observed in sediment traps, although chl a, fucoxanthin and 19'-hexanoyloxyfucoxanthin were detected in smaller concentrations as well as traces of chlorophyll b (chl b). In deep water, fucoxanthin and 19'-hexanoyloxyfucoxanthin were the only accessory pigments present while total phaeopigment/chl a molar ratios >1 reflected the active transformation of fine phytogenic material at depth. High particulate organic carbon (POC)/chl a ratios (>100 in surface water; >1000 in deep water) suggested that phytoplankton was a relatively small component of the total carbon biomass down the water column. Using simple budget calculations, we determined that 58 to 65% of the chl a produced in the upper 100 m accumulated in the water column over both experiments. During Expt 1, 29% of the chl a sedimented out, mostly as phaeopigment, at 100 m (24%), and 6% was degraded to colourless residues in the water column. In contrast, only 12% of the chl a sedimented in Expt 2, while 20% was degraded to colourless residues

Costs and benefits to European shipping of ballast-water and hull-fouling treatment: Impacts of native and non-indigenous species

Maritime transport and shipping are impacted negatively by biofouling, which can result in increased fuel consumption. Thus, costs for fouling reduction can be considered an investment to reduce fuel consumption. Anti-fouling measures also reduce the rate of introduction of non-indigenous species (NIS). Further mitigation measures to reduce the transport of NIS within ballast water and sediments impose additional costs. The estimated operational cost of NIS mitigation measures may represent between 1.6% and 4% of the annual operational cost for a ship operating on European seas, with the higher proportional costs in small ships. However, fouling by NIS may affect fuel consumption more than fouling by native species due to differences in species’ life-history traits and their resistance to antifouling coatings and pollution. Therefore, it is possible that the cost of NIS mitigation measures could be smaller than the cost from higher fuel consumption arising from fouling by NIS

Low salinity as a biosecurity tool for minimizing biofouling on ship sea chests

Biofouling is a major vector in the transfer of non-native species around the world. Species can be transported on virtually all submerged areas of ships (e.g. hulls, sea chests, propellers) and so antifouling systems are used to reduce fouling. However, with increased regulation of biocides used in antifoulants (e.g. the International Maritime Organization tributyltin ban in 2008), there is a need to find efficient and sustainable alternatives. Here, we tested the hypothesis that short doses of low salinity water could be used to kill fouling species in sea chests. Settlement panels were suspended at 1.5 m depth in a Plymouth marina for 24 months by which time they had developed mature biofouling assemblages. We exposed these panels to three different salinities (7, 20 and 33) for 2 hours using a model sea chest placed in the marina and flushed with freshwater. Fouling organism diversity and abundance were assessed before panels were treated, immediately after treatment, and then 1 week and 1 month later. Some native ascidian Dendrodoa grossularia survived, but all other macrobenthos were killed by the salinity 7 treatment after 1 week. The salinity 20 treatment was not effective at killing the majority of fouling organisms. On the basis of these results, we propose that sea chests be flushed with freshwater for at least 2 hours before ships leave port. This would not cause unnecessary delays or costs and could be a major step forward in improving biosecurity

Reconciliation of the carbon budget in the ocean’s twilight zone

Photosynthesis in the surface ocean produces approximately 100 gigatonnes of organic carbon per year, of which 5 to 15 per cent is exported to the deep ocean1, 2. The rate at which the sinking carbon is converted into carbon dioxide by heterotrophic organisms at depth is important in controlling oceanic carbon storage3. It remains uncertain, however, to what extent surface ocean carbon supply meets the demand of water-column biota; the discrepancy between known carbon sources and sinks is as much as two orders of magnitude4, 5, 6, 7, 8. Here we present field measurements, respiration rate estimates and a steady-state model that allow us to balance carbon sources and sinks to within observational uncertainties at the Porcupine Abyssal Plain site in the eastern North Atlantic Ocean. We find that prokaryotes are responsible for 70 to 92 per cent of the estimated remineralization in the twilight zone (depths of 50 to 1,000 metres) despite the fact that much of the organic carbon is exported in the form of large, fast-sinking particles accessible to larger zooplankton. We suggest that this occurs because zooplankton fragment and ingest half of the fast-sinking particles, of which more than 30 per cent may be released as suspended and slowly sinking matter, stimulating the deep-ocean microbial loop. The synergy between microbes and zooplankton in the twilight zone is important to our understanding of the processes controlling the oceanic carbon sink

The Western Channel Observatory: a century of physical, chemical and biological data compiled from pelagic and benthic habitats in the western English Channel

Abstract. The Western Channel Observatory (WCO) comprises a series of pelagic, benthic and atmospheric sampling sites within 40 km of Plymouth, UK, that have been sampled by the Plymouth institutes on a regular basis since 1903. This longevity of recording and the high frequency of observations provide a unique combination of data; for example temperature data were first collected in 1903, and the reference station L4, where nearly 400 planktonic taxa have been enumerated, has been sampled on a weekly basis since 1988. While the component datasets have been archived, here we provide the first summary database bringing together a wide suite of the observations. This provides monthly average values of some of the key pelagic and benthic measurements for the inshore site L4 (50∘15.00′ N, 4∘13.02′ W; approx. depth 55 m), the offshore site E1 (50∘02.00′ N, 4∘22.00′ W; approx. depth 75 m) and the intermediate L5 site (50∘10.80′ N, 4∘18.00′ W; approx. depth 58 m). In brief, these data include the following: water temperature (from 1903); macronutrients (from 1934); dissolved inorganic carbon and total alkalinity (from 2008); methane and nitrous oxide (from 2011); chlorophyll a (from 1992); high-performance liquid chromatography (HPLC)-derived pigments (from 1999); <20 µm plankton by flow cytometry, including bacteria (8 functional groups from 2007); phytoplankton by microscopy (6 functional groups from 1992); microplankton and mesozooplankton from FlowCam (6 groups from 2012); Noctiluca sp. dinoflagellate (from 1997); mesozooplankton by microscopy (8 groups from 1988); Calanus helgolandicus egg production rates (from 1992); fish larvae from the Young Fish Trawl survey (4 groups from 1924); benthic macrofauna (4 groups from 2008); demersal fish (19 families from 2008); blue shark, Prionace glauca (from 1958); and 16S alpha diversity for sediment and water column (from 2012). These data have varying coverage with respect to time and depth resolution. The metadata tables describe each dataset and provide pointers to the source data and other related Western Channel Observatory datasets and outputs not compiled here. We provide summaries of the main trends in seasonality and some major climate-related shifts that have been revealed over the last century. The data are available from the Data Archive for Seabed Species and Habitats (DASSH): https://doi.org/10.17031/645110fb81749 (McEvoy and Atkinson, 2023). Making these data fully accessible and including units of both abundance and biomass will stimulate a variety of uptakes. These may include uses as an educational resource for projects, for models and budgets, for the analysis of seasonality and long-term change in a coupled benthic–pelagic system, or for supporting UK and north-eastern Atlantic policy and management

The Western Channel Observatory: a century of physical, chemical and biological data compiled from pelagic and benthic habitats in the western English Channel

The Western Channel Observatory (WCO) comprises a series of pelagic, benthic and atmospheric sampling sites within 40 km of Plymouth, UK, that have been sampled by the Plymouth institutes on a regular basis since 1903. This longevity of recording and the high frequency of observations provide a unique combi�nation of data; for example temperature data were first collected in 1903, and the reference station L4, where nearly 400 planktonic taxa have been enumerated, has been sampled on a weekly basis since 1988. While the component datasets have been archived, here we provide the first summary database bringing together a wide suite of the observations. This provides monthly average values of some of the key pelagic and benthic measure�ments for the inshore site L4 (50◦15.000 N, 4◦13.020 W; approx. depth 55 m), the offshore site E1 (50◦02.000 N, 4 ◦22.000 W; approx. depth 75 m) and the intermediate L5 site (50◦10.800 N, 4◦18.000 W; approx. depth 58 m). In brief, these data include the following: water temperature (from 1903); macronutrients (from 1934); dissolved inorganic carbon and total alkalinity (from 2008); methane and nitrous oxide (from 2011); chlorophyll a (from 1992); high-performance liquid chromatography (HPLC)-derived pigments (from 1999); <20 µm plankton by flow cytometry, including bacteria (8 functional groups from 2007); phytoplankton by microscopy (6 functional groups from 1992); microplankton and mesozooplankton from FlowCam (6 groups from 2012); Noctiluca sp. dinoflagellate (from 1997); mesozooplankton by microscopy (8 groups from 1988); Calanus helgolandicus egg production rates (from 1992); fish larvae from the Young Fish Trawl survey (4 groups from 1924); benthic macrofauna (4 groups from 2008); demersal fish (19 families from 2008); blue shark, Prionace glauca (from 1958); and 16S alpha diversity for sediment and water column (from 2012). These data have varying coverage with respect to time and depth resolution. The metadata tables describe each dataset and provide pointers to the source data and other related Western Channel Observatory datasets and outputs not compiled here. We pro�vide summaries of the main trends in seasonality and some major climate-related shifts that have been revealed over the last century. The data are available from the Data Archive for Seabed Species and Habitats (DASSH): https://doi.org/10.17031/645110fb81749 (McEvoy and Atkinson, 2023). Making these data fully accessible and including units of both abundance and biomass will stimulate a variety of uptakes. These may include uses as an educational resource for projects, for models and budgets, for the analysis of seasonality and long-term change in a coupled benthic–pelagic system, or for supporting UK and north-eastern Atlantic policy and management

Grazing by Calanus helgolandicus and Para-Pseudocalanus spp. on phytoplankton and protozooplankton during the spring bloom in the Celtic Sea

Feeding rates and selectivity of the calanoid copepods Calanus helgolandicus and Para-Pseudocalanus spp. on natural assemblages of microplankton were evaluated in the English Channel and western Celtic Sea during non-bloom and bloom conditions in April 2002. Ingestion rates of total chlorophyll-a were low at non-bloom stations where the phytoplankton community was dominated by cells &lt; 5 ?m in length and higher during the bloom when the &gt; 5 ?m size fraction was dominant. Protozooplankton contributed to the copepod diet in all experiments, C. helgolandicus clearance and ingestion rates were highest for the ciliate Myrionecta rubra (626–1347 ml cop? 1 d? 1; 0.3–27 ?g C cop? 1 d? 1). C. helgolandicus ingested between 1 and 18 ?g C cop? 1 d? 1 (1–12% body C) from phytoplankton + protozooplankton food sources. The total carbon ingested by Para-Pseudocalanus spp. was lower (0.5–6 ?g cop? 1 d? 1) but this was equivalent to between 6 and 78% of body carbon being ingested daily. Our data suggest that C. helgolandicus selected prey according to size; this was not the case for Para-Pseudocalanus spp. which became more selective as chlorophyll-a concentration increased. Grazing impact of the entire copepod community on protozooplankton was assessed. We found that at non-bloom stations between 12 and 17% of the protozooplankton community was being removed daily by the copepod community, whereas during the peak of the bloom the proportion being removed daily was only 2%. We conclude that during the spring bloom period copepods gained the majority of their carbon from phytoplankton ingestion but during non-bloom periods, protozooplankton and the ciliate M. rubra made a significant contribution to copepod diet

Are we at Last Ready to Begin Controlling the Global Spread of Aquatic Invasives?

The question really should be: are we really serious about controlling the global spread of aquatic invasives? Given that it has so far taken over 11 years to even get close to ratifying the International Maritime Organisation (IMO) Ballast Water Convention, the answer has to be ‘not really’! Coupled with this, we are also aware that another significant vector of transport for aquatic invasives is hull fouling on ships, which is currently unregulated on a global scale