ARTICLE | doi:10.20944/preprints202302.0396.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Convolutional Neural Network; Ensemble Learning; Transfer Learning; Fine-tuning; Plankton Classification; foraminifera
Online: 23 February 2023 (03:37:23 CET)
This paper presents a study of an automated system for identifying planktic foraminifera at the species level. The system uses a combination of deep learning methods, specifically Convolutional Neural Networks (CNNs), to analyze digital images of foraminifera taken at different illumination angles. The dataset is composed of 1437 groups of sixteen grayscale images, one group for each foraminifer, that are then converted to RGB images with various processing methods. These RGB images are fed into a set of CNNs, organized in an Ensemble Learning (EL) environment. The ensemble is built by training different networks using different approaches for creating the RGB images. The study finds that an ensemble of CNN models trained on different RGB images improves the system's performance compared to other state-of-the-art approaches. The proposed system was also found to outperform human experts in classification accuracy.
ARTICLE | doi:10.20944/preprints202212.0427.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Plankton; Monitoring; Harmful algae; microscopic; genetic; Western Channel
Online: 22 December 2022 (11:34:13 CET)
Plankton monitoring by microscopy offers long-term ecological perspective of plankton com-munities but different detection approaches are biased uniquely. Genetic identification of marine plankton has become standard but is still not used in routine monitoring. This study assessed the diversity of plankton taxa using 18S high throughput sequencing from 2011-2012 from small-volume (~200ml) samples from the Water and Microplankton Sampler (WaMS) deployed on the Continuous Plankton Recorder platform (CPR). The 18S-HTS survey revealed a bias towards heterotrophic taxa, and phototrophs under 10µm within the photosynthetic community. In comparison with phytoplankton microscopic counts from the CPR survey and Western Channel Observatory station L4, only 8-12 taxonomic families were common to all three surveys, with a bias towards larger diatoms and dinoflagellate taxa in microscopy surveys. The WaMS survey detected a contrasting but complementary taxa set to that of microscopic surveys. Additional Quantitative PCR was carried out on the picoeukaryotic pelagophyte, Aureococcus anophagefferens, and the nanoeukaryotic potential harmful algae, Pseudo-nitzschia delicatissima, from 2011-2013. This confirmed the persistence presence of A. anophagefferens in the Western Channel and an elevated abundance of both species in 2011. Species specific seasonality were distinct from those of aggregrate phytoplankton groups.
ARTICLE | doi:10.20944/preprints202207.0332.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Plankton; Monitoring; Harmful algae; microscopic; genetic; Western Channel
Online: 22 July 2022 (03:33:40 CEST)
Plankton monitoring by microscopy offers long-term ecological perspective of plankton communities but is biased towards those organisms that can be distinguished using the microscope. Genetic identification of marine plankton has become standard but is still not used. This study is a comprehensive study genetically measured taxa in the Western Channel of UK using a small-volume automated water sampler deployed on the CPR platform. The study present one year of high-throughput sequencing data focussing on smaller plankton and separate community to that measured by microscopy that can complement each other for a holistic view of plankton. Quantitative tests of two harmful algae show relatively high abundance of the Pelagophyte Aureococcus anophagefferens during 2011 with low nitrite levels. Three years of Pseudo-nitzschia delicatissima quantitative monitoring also shows a greater abundance of this potentially harmful taxa in 2011. Flow cytometry reveals distinct seasonal cycles with distinct timings.
ARTICLE | doi:10.20944/preprints202007.0594.v2
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Crustacea; Zooplankton; Plankton; Pacific Ocean; Larvae; DNA barcoding
Online: 16 April 2021 (11:23:51 CEST)
Determining the DNA sequencing of a small element in the mitochondrial DNA (DNA barcoding) makes it possible to easily identify individuals of different larval stages of marine crustaceans without the need for laboratory rearing. It can also be used to construct taxonomic trees, although it is not yet clear to what extent this barcode-based taxonomy reflects more traditional morphological or molecular taxonomy. Collections of zooplankton were made using conventional plankton nets in Newport Bay and the Pacific Ocean near Newport Beach, California (Lat. 33.628342, Long. -117.927933) between May 2013 and January 2020, and individual crustacean specimens were documented by videomicroscopy. Adult crustaceans were collected from solid substrates in the same areas. Specimens were preserved in ethanol and sent to the Canadian Centre for DNA Barcoding at the University of Guelph, Ontario, Canada for sequencing of the COI DNA barcode. From 1042 specimens, 544 COI sequences were obtained falling into 199 Barcode Identification Numbers (BINs), of which 76 correspond to recognized species. The results show the utility of DNA barcoding for matching life-cycle stages as well as for documenting the diversity of this group of organisms.
ARTICLE | doi:10.20944/preprints202209.0260.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Mollusks; gastropods; Zooplankton; Plankton; Pacific Ocean; larvae; DNA barcoding
Online: 19 September 2022 (04:57:36 CEST)
The life cycles and biodiversity of Pacific coast gastropods were analyzed by videomicroscopy and DNA barcoding of indi-viduals collected from tide pools and in plankton nets from a variety of shore stations. In many species (Families Calyptrae-idae, Cerithiopsidae, Strombidae, Vermetidae, Columbellidae, Nassariidae, Olivellidae, Hermaeidae, Onchidorididae, Gas-tropteridae, Haminoeidae), the free-swimming veligers were recovered from plankton collections; in Roperia poulsoni (family Muricidae) veligers were usually recovered from egg sacs where they had been retained although some escapees were found in plankton collections; in Pteropurpura festiva (family Muricidae) free-living veligers were also found; and in Atlanta californiensis (family Atlantidae) both veligers and adults were obtained from plankton collections making this a holoplank-tonic species. The results confirm that DNA barcoding using the COI barcode is a useful strategy to match life-cycle stages within species as well as to identify species and to document the level of biodiversity within the gastropods.
ARTICLE | doi:10.20944/preprints202205.0013.v1
Subject: Physical Sciences, Acoustics Keywords: sea water; bubbles; plankton; sound scattering; sound attenuation; acoustic spectroscopy
Online: 4 May 2022 (14:16:08 CEST)
The presence of bubbles near the sea surface under certain conditions leads to abnormal sound scattering and a significant change in the acoustic properties of the upper layer of the sea. The article presents some results of sound scattering studies under various sea conditions, up to stormy conditions, when extensive bubble clouds arise. By the method of unsteady acoustic spectroscopy, data on the size distribution of bubbles at various depths have been obtained, which can be described by a power function with exponential decay at small bubble sizes of the order of 10 microns. Estimates of the gas content in bubble clouds and their influence on the acoustic characteristics of the upper layer of the sea have been carried out. It is shown that at sufficiently high concentrations, sharp increases in absorption and dispersion of the sound velocity are observed. Modeling of sound propagation in the presence of a quasi-homogeneous bubble layer shows that it leads both to a change in the laws of the average decay of the sound field along the sound propagation path and to a change in the shallow spatial structure of the field.