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Laboratory for Ecology and Evolutionary Biology of Aquatic Organisms (LEEBAO)

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As of 01.11.2022

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General information

Name of the project: Biology of marine invertebrates

Goals and objectives

Research directions: Research of biological resources of the World Ocean

Project objective: Complex research of biological diversity and biological resources of invertebrates of Far Eastern seas of Russia at all levels of organization of living matter – from biocenotic to molecular.

The practical value of the study

Scientific results:
  1. A comprehensive study of the biological diversity of individual mass groups of phyto- and zoobentos of sand beach coastlines and estuary zones of the Sea of Japan to determine feeding links in these ecosystems that characterize the role of individual trophic and taxonomic groups of hydrobionts in the regulation of the decomposition of organic matter and energy flow.
  2. Methods have been developed and implemented for the laboratory diagnostics of the states of populations of commercial marine invertebrates to detect various pathologies both for implementing express tests in marine farms and for preserving the marine biodiversity. We studied the mechanisms of the activation of expression of  growth factor genes, which will help to solve the problem of increasing the proliferative activity of cells in the conditions of a culture of cells of marine invertebrate animals – producers of mineral structures. We have developed and successfully applied methods for the preparation of samples of tissues of nematodes for immunochemical and immunocytochemical analysis
  3. We have assessed the efficiency of new immunostimulating complexes (tubular immunostimulating complexes based on biologically active substances produced from marine hydrobionts) as adjuvant carriers of viral antigens. We have demonstrated their good prospects for use in the development of next-generation nanovaccines for vaccination against epidemic diseases. We also demonstrated the high anti-tumor activity if the created TI complexes. A new technology for the cryoconservation of marine hydrobionts at ultra-low temperatures allowing to significantly increase the output of viable cells.
  4. We have organized and staged a research expedition to study the regenerative potential of  coastal ecosystems of the Kamchatka peninsula after the harmful algal bloom (HAB) in the autumn of 2020. It has been demonstrated that aquasoils is characterized by the sand granulometric composition and a low content of organic matter. According to data on the content of acid-soluble forms of heavy metals and a comparison of those with the MPC and APC, no exceedances were detected, except for aquasoils from the Listvennichnaya Bay for arsenic, where we could observe an increase of 24 per cent of the APC. No exceedances of Clark contents in all the elements were found. The radiation situation on the studied territory is characterized as favorable. We found individual regions of local contamination with organic matter in the center of the bays Listvennichnaya and Vilyuchinskaya, the Malaya Lagernaya bay, the Spaseniya bay, the surroundings of the Ozernovskiy village. According to the concentrations of phosphorus, the coastal marine waters of the Kamchatka peninsular have a mesotrophic status. On the litoral near the Ozerkovskiy village  at depths of 5 meters and deeper in all the other investigated regions a mussel-algal community is formed with a mean biomass of more than 3000 g/m2, unlike the Malaya Lagernaya bay, where at a depth 3 meters on a rocky reef we found a concentration of globular sea urchins and sea anemones with a biomass of more than 1000 g/m2. For all the other studied stations the biomass of echinoderms amounted on average to about 3 g/m2 (0,1%). Relying on data on the overall population of microorganisms, surface waters washing the Kamchatka peninsula can be attributed to class 4-5 of water quality, characterizing them as polluted, locally muddy. According to data on the numbers of colony-forming heterotrophic microorganisms, the waters are characterized as α/β-mesosaprobic, enriched with organic compounds. Bacteria of the sanitary-indicative group are found in sufficient amounts, which indicates biological and fecal contamination of the waters. An analysis of the microorganisms count growing in environments with crude oil allows to classify the waters of the majority of the aquatic area as weakly polluted with local regions of anthropogenic press. Phenol-resistant microorganisms found at all the reserched stations in quite high concentrations indicate a noticeable and significant contamination of the environment with this class of pollutants. On the coast of the Kanchatka peninsula we found an almost significant contamination with persistent organic pollutants (POPs). Despite the quite wide range of concentrations, no pollution levels that are hazardous for the environment were found. Registering organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) at all the stations indicates the influence of the atmospheric transfer and the existence of a global background of pesticides on the planet. A set of conservative parts of DNA characteristic only of the Dinoflagellates group and additionally for toxic species of Dinoflagellates of the Far Eastern seas of Russia. The collected locuses will be used for the quantitative assessment of the concentration of Dinoflagellates cells and toxic species of Dinoflagellates using real-time PCR and next-generation sequencing, including with the use of single-cell sequencing methods.
  5. We have developed the EXONtools software pipeline for analyzing exonic sequencing  data, mainly aimed at the research of the genomes of non-model marine organisms. EXONtools is a set of 25 software modules performing various tasks for three  sequential stages of exon sequencing: 1) creating a pseudo-reference based on de novo assmebly of transcriptomes and its annotation; 2) designing exon matrices for the synthesis of hybridization probes with affine biotin tag; 3) assembling, annotating and aligning exons for a subsequent population analysis of nucleotide polymorphisms and various genomic artifact. For each separate module we proposed optimal algorithms implemented using the Python programming language. For instance, we developed algorithms for designing reference regions of the genome on the basis of a combination of annotated transcriptomes («pseudo-reference»), searching for exons and rapidly creating hybridization probes for tens of thousands of locuses. While implementing the project, we also adapted the pipeline for working with UCE data and RAD sequencing data as well as for conducting simple reference assembly in one of its modules. To test the developed method we synthesized hybridization probes for fish of the orders Gobiiformes and Salmoniformes, which were later used to produce population genome data over large sets of individuals. We also conducted an in silico comparative analysis    of the efficiency the EXONtools pipline using the existing annotated genomes of model species. 

Implementation of research results:

The created pipeline for exon sequencing data analysis can be used in genome research centers that provide services in searching and annotating nucleotide polymorphisms using next-generation sequencing platforms. The experimental design of a method of exon sequencing implies the use of hybridization probes (biotinylated oligonucleatides) for producing encoding regions of the genome of any non-model organism. The creation of matrices of hybridization probes for any non-model organism and the selection of optimal experimental parameters for their hybridization is is one of the key stages of the operation of the  EXONtools software pipeline. 

Education and career development:

  • One Doctor of Sciences and 15 Candidate of Sciences dissertations have been prepared and defended.
  • From 2010 to 2018 on the grounds of the Laboratory 10 new education programs were implemented in the primary domain of our project: «Regional environmental problems», «Introduction to the biology of the neuron», «Maine ecology», «Summer field practice in assessing the quality of natural waters», «Flow cytometry as a tool for the analysis of  cell populations», «Comparative anatomy of invertebrates», «Introduction to marine ecology», «Theory and methodology of scientific research», «Introduction to the molecular ecology of microorganisms», «Methods of cytological research».
  • Sine 2020 the research team of the Laboratory has prepared and implemented  new education disciplines, including lectures and case studies in «Population biology», «Phylogenetics», «Quantitative genetics», «Molecular biology», «Transcriptomics» and «Comparative genomics».
  • Several online master classes have been delivered for attendees of the «Sirius» education center.
  • For students of the «Sirius» university we are currently implementing a master’s and postgraduate degree in «Computational biology and bioinformatics».
  • At the «Sirius» University and the Higher School of Economics, as part of the implementation of the additional training programs «Basics of bioinformatics and mathematical biology», «Practical bioinformatics», «Modern bioinformatics» we have prepared and delivered education modules in the disciplines «Molecular biology», «Transcriptomics» and «Comparative genomics». 

Organizational and structural changes: 

The Laboratory’s equipment is part of the Center for the Collective Use of Scientific Equipment of the Far Eastern Federal University. The Laboratory features a wide range of high-tech equipment for conducting research in biology. 

Other results: 

Employees of the LaboratoryKuril basin collaborated with the Far Eastern Branch of the Russian Academy of Sciences participated in major sea expedition: to the Sea of Ohkotsk (the Kuril trench) and the Bering Sea (the Piypa volcano) (SokhoBio, SoJaBio) within the international research program CeDAMar (Census of the Diversity of Abyssal Marine Life); to the area of the Kuril–Kamchatka Trench in the northwestern Pacific (KuramBio I and II). During the expiditions we demonstrated the efficiency of the use of remote-controlled submersibles in hydrobiology research and for the assessment of the state marine bioresouces. As a result of the research we demonstrated the high biological diversity of deep-sea regions the Pacific ocean, described a signifiant number of new species. 


Russian-Vietnamese Tropical Research  and Technology Center: performing a complex of research works on the topic «Diversity of marine benthic invertebrate hydrobionts in communities of sea grass along a wide gradient on the example of individual taxons of micro- and meiofauna». 

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atopkin, d.m., semenchenko, a.a., solodovnik, d.a., ivashko, y.i. and vinnikov, k.a.
First next-generation sequencing data for Haploporidae (Digenea: Haploporata): characterization of complete mitochondrial genome and ribosomal operon for Parasaccocoelium mugili Zhukov, 1971. Parasitology Research 120(6): 2037-2046 (2021).
ezhova o.v., ershova n.a., malakhov v.v.
Microscopic anatomy of the axial complex and associated structures in the sea cucumber Chiridota laevis Fabricius, 1780 (Echinodermata, Holothuroidea). Zoomorphology 136(2): 205–217 (2017).
odintsova n.a., boroda a.v., maiorova m.a., yakovlev k.v.
The death pathways of mussel larval cells after a freeze-thaw cycle. Cryobiology 77: 41–49 (2017).
oleinik, a.g., skurikhina, l.a., kukhlevsky, a.d. and semenchenko, a.a.
The first complete mitochondrial genomes of two species of charr, Salvelinus boganidae and Salvelinus elgyticus, from Lake El’gygytgyn (Chukotka). Polar Biology 44(6): 1209-1217 (2021).
orlova, t.y., aleksanin, a.i., lepskaya, e.v., efimova, k.v., selina, m.s., morozova, t.v., stonik, i.v., kachur, v.a., karpenko, a.a., vinnikov, k.a. and adrianov, a.v.
A massive bloom of Karenia species (Dinophyceae) off the Kamchatka coast, Russia, in the fall of 2020. Harmful Algae 120: 102337 (2022).
shibneva, s.y., skriptsova, a.v. and semenchenko, a.a.
Molecularly assisted taxonomic studies of marine red algae from the north-western Pacific: establishing the ordinal and family positions of the genus Lukinia and the monospecific status of the genus Sparlingia (Rhodymeniales). Phycologia 61(1) 37-44 (2022).
vinnikov, k.a., thomson, r.c. and munroe, t.a.
Revised classification of the righteye flounders (Teleostei: Pleuronectidae) based on multilocus phylogeny with complete taxon sampling. Molecular phylogenetics and evolution 125: 147-162 (2018).
zograf j.k., pavlyuk o.n., trebukhova yu.a., nguyen dinh tu.
Revision of the genus Parasphaerolaimus (Nematoda: Sphaerolaimidae) with description of new species. Zootaxa 4232(1): 58 (2017).
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