About

Dr. Denis Grouzdev is a Research Associate Professor at the Marine Animal Disease Laboratory (MADL) with expertise in genomics, computational biology, and bioinformatics. His scientific background includes microbiology, biotechnology, and molecular biology, with a Ph.D. in biotechnology obtained in 2014 from Lomonosov Moscow State University, Russia. His dissertation focused on the molecular basis of bacterial magnetic particles biotechnology, exploring microbial biomineralization, microbial magnetotaxis, and their ecological functions. His research at MADL involves the genomic characterization of infectious microbes and their shellfish hosts, emphasizing host-parasite interactions, genome-wide association studies, and genomic selection. Dr. Grouzdev's work contributes to understanding the genomic mechanisms underlying infectious diseases in shellfish, supporting efforts in disease resistance and environmental impact assessments.

Research topics

• Biology
• Genetics
• Biochemistry
• Botany
• Microbiology
• Paleontology
• Astrobiology
• Evolutionary biology
• Anatomy

Selected publications

• Transcriptomic characterization of mucosal hemocytes in the eastern oyster (Crassostrea virginica) underlines their potential role as immune sentinels

  Frontiers in Immunology · 2026-03-30

  articleOpen access

  Substantial progress has been made in understanding hemocytes within the hemolymph (herein referred to as circulatory hemocytes), which are essential for immune defense and various physiological functions in bivalve mollusks. Yet, our knowledge of peripheral immunity, particularly the role of hemocytes associated with mucosal surfaces covering pallial (gills, mantle) organs (herein referred to as mucosal hemocytes), remains limited. While mucosal and circulatory hemocytes share similar morphologies, they exhibit distinct functional profiles and cell surface epitopes. The molecular mechanisms underlying these functional differences remain poorly understood. To address this knowledge gap, we characterized gene expression profiles (using RNA sequencing) in granulocytes and agranulocytes isolated via flow cytometry from hemolymph and mucus covering pallial tissues of the eastern oyster, Crassostrea virginica . Mucosal hemocytes showed overexpression of genes related to cell motility, cytokine activity, signaling, and cell adhesion, supporting the hypothesis that they may have sentinel functions. Despite a consistent dichotomy in gene expression between granulocytes and agranulocytes across both body fluids, it was more pronounced in circulatory hemocytes. Circulatory granulocytes showed functions linked to phagocytosis and pathogen killing, whereas circulatory agranulocytes overexpressed genes associated with mitosis and early inflammation compared to their mucosal counterparts. To our knowledge, this is the first study combining flow cytometry sorting and transcriptomic methods to characterize hemocytes from different body fluids in a marine invertebrate. Results underline the potential role of mucosal hemocytes as immune sentinels, although more studies, possibly using single-cell transcriptomic methods and functional assays associated with pathogen challenge experiments, are needed to probe their specific functions.

  PublisherOA PDFDOI

• Magnetotactic <i>Bdellovibrionota</i> from a ferruginous spring

  ISME Communications · 2026-04-22

  articleOpen access

  Abstract Magnetotactic bacteria form a highly diverse group of microorganisms, yet early exploration of their diversity was largely centered on the Pseudomonadota. More recently, metagenomic studies have revealed that magnetotaxis, a form of chemotaxis guided by Earth's magnetic field, is widespread in other deep-branching phyla for which little to no ecological or biological information is available beyond that inferred from their genomes. For most of them, the morphology, ultrastructure and magnetosome chain characteristics responsible for the magnetic guidance remain unknown. While screening extreme environments for novel magnetotactic species, we observed magnetotactic Bdellovibrionota in the anoxic and ferruginous sediments of the Fontaine Goyon spring (France). We characterized their cell morphology and ultrastructure using magnetic enrichment, a single-cell sorting approach, and high-resolution electron microscopy. Cells display the morphology typical of the few predatory bacteria described in this phylum, and biomineralize, on average, five irregularly faceted, bullet-shaped magnetite magnetosomes along the concave side of the cell. Metagenomic analysis of approximately one hundred cells revealed a potentially predatory and heterotrophic lifestyle adapted to low-O2 conditions. It also suggests a flexible respiratory metabolism under varying redox conditions, using iron as an alternative terminal electron acceptor. Exploring the diversity of Bdellovibrionota in public databases, we found 21 metagenome-assembled-genomes containing magnetosome genes. None of them harbor the canonical mamK actin-like gene implicated in aligning magnetosomes in described magnetotactic models. Affiliated to an undescribed class, we propose a classification scheme for the magnetotactic Bdellovibrionota species representing the class Bdellonasia class nov., for which no species had been formally described.

  PublisherDOI

• Survival of the fittest: genomic investigations of the bay scallop reveal a shift in population structure through a summer mortality event

  BMC Genomics · 2025-02-15

  articleOpen access1st authorCorresponding

  BACKGROUND: Understanding the genetic basis of resilience in marine organisms is critical for conservation and management, particularly in the face of escalating environmental stress and disease outbreaks. The bay scallop Argopecten irradians is a commercially and recreationally important shellfish species found in estuarine and coastal environments of the United States from New England to the Gulf of Mexico. In New York, adult bay scallop populations have been decimated every summer since 2019 leading to the collapse of their fishery. These mortality events were associated with annual outbreaks of an undescribed apicomplexan parasite recently named Bay Scallop Marosporida (BSM) that disrupts scallop kidneys. RESULTS: This study investigates host-pathogen interactions and assesses changes in population structure during BSM-associated mortality events. The research compared wild and aquacultured scallops used for stock enhancement in New York, revealing significant change in population structures throughout the mortality outbreak. The results underscore the selective pressures exerted by BSM infection and environmental stressors, as evidenced by shifts in genetic divergence and allele frequencies particularly in genes associated with kidney function, stress and infection response. Through a detailed genomic and population genetic approach, this research represents a unique case study highlighting the impact of disease on marine biodiversity and advances our understanding of the impact of summer mortality events on the scallop population in NY. CONCLUSIONS: This study highlights changes in the genomic structure of bay scallops during a BSM-associated mortality event. Identified mutations (such as the one in the nephrocystin-3-like gene) represent prime candidates for specific targeted investigations to link genotypes to phenotypes. By integrating genomic and epidemiological data, the research provides a basis for understanding the impact of disease on scallop biodiversity. These findings may help guide conservation strategies for sustainable fisheries in the face of environmental change and disease outbreaks.

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• Cryobacterium Inferilacus sp. nov., a Pshychrophilic Ureolitic Bacterium From Lake Untersee in Antarctica

  Microorganisms · 2025-04-25

  articleOpen access

  The psychrophilic aerobic heterotrophic bacterium, strain 1639T, was isolated from the low-temperature Lake Untersee in Antarctica. The bacterium was Gram-positive, non-motile, yellow–green-pigmented, non-spore-forming, and a pleomorphic rod. Growth was observed at temperatures of 0–25 °C with an optimum at 10 °C. The strain used urea as a nitrogen source. The major fatty acids were i-C16:0 (49.69%), ai-C15:0 (17.59%), and C16:1 branched (12.03%). Identified polar lipids were phosphatidylglycerols and a glycolipid. The respiratory quinone was determined to be MK-10. The genomic DNA G+C content was 68.03 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1639T was a member of the genus Cryobacterium, with the highest sequence similarity to C. arcticum SK1T (98.4%), C. soli GCJ02T (98.4%), C. lactosi Sr59T (98.3%), C. zongtaii TMN-42T (98.2%), and C. adonitolivorans RHLS22-1T (98.1%). The ANI and the DNA–DNA hybridization estimate values between strain 1639T and all type strains of species of the genus Cryobacterium were in the range of 84.3–87.8% and 20.5–40.3%, respectively. The combined genotypic and phenotypic data indicate that strain 1639T represents a novel species within the genus Cryobacterium, for which the name Cryobacterium inferilacus sp. nov. is proposed with the type strain 1639T (=KCTC 59142T, =VKM Ac-2907T, UQM 41460T).

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• Genome-wide association mapping for heat shock tolerance in Mercenaria mercenaria through SNP microarray analysis

  BMC Genomics · 2025-05-30 · 2 citations

  articleOpen access

  Abstract Background The northern quahog Mercenaria mercenaria is a major aquaculture species on the US East Coast, and heat resistance is the most sought trait for aquaculture. This study aimed to establish a genome-wide association for heat tolerance using a 66K SNP array for M. mercenaria . Quahogs from three farms were combined for a heat challenge at 1 °C per day from 24 °C to 35 °C and stay for two days (Phase I), decreasing to 27 °C in 24 h, to 24 °C in another 24 h, and maintaining at 24 °C (Phase II) until no one dead within 48 h at 24 °C (Phase III). Dead and live quahogs were sampled for genotyping using the SNP array. Results During the heat challenge, different mortalities among the quahogs from the three farms were identified at 38, 46, and 55% at Phase I, and 36, 30, and 29% at Phase II. For the survivors (Phase III), no changes were found in body weight before and after the heat shock challenges ( p &lt; 0.265). The PCA analyses of SNP frequencies indicated significant genetic differences associated with quahog survival under heat stress across the different farms. The heritability of the heat tolerance was 0.680 ± 0.063. GWAS analysis indicated that one SNP exhibited a significant association with the time-to-death trait on chromosome 7 ( p = 1.98 × 10 − 5 ). More significant SNPs ( p &lt; 10 − 3.5 ) were inside genes that have been reported to function in heat tolerance such as serine/threonine-protein kinase 31 and carbohydrate sulfotransferase 11 , and some genes found within 50 K bp far from SNP sites have a relationship with heat tolerance such as toll-like receptors 4 and 6 ( TLRs 4 and TLRs 6 ), uracil-DNA glycosylase , and a disintegrin and metalloproteinase with thrombospondin motifs gon-1 ( ADAMT s). Conclusion The fastStructure analysis revealed the proportions of different ancestral components within the quahogs from different farming stocks, highlighting that the genetic factors may contribute to their varying survival rates under heat stress. The associated genes have potential roles in immune response, cellular stress, and tissue repair. The findings highlighted the power of high-throughput approaches for the identification of superior quahog genotypes for further breeding.

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• Sulfate-Reducing Bacteria Isolated from an Oil Field in Kazakhstan and a Description of Pseudodesulfovibrio karagichevae sp. nov.

  Microorganisms · 2024-12-11 · 5 citations

  articleOpen access

  Sulfidogenic bacteria cause numerous issues in the oil industry since they produce sulfide, corroding steel equipment, reducing oil quality, and worsening the environmental conditions in oil fields. The purpose of this work was to isolate and taxonomically identify the sulfidogenic bacteria responsible for the corrosion of steel equipment at the Karazhanbas oil field (Kazakhstan). In this study, we characterized five sulfidogenic strains of the genera Pseudodesulfovibrio, Oleidesulfovibrio, and Acetobacterium isolated from the formation water of the Karazhanbas oil field (Kazakhstan). Sulfate-reducing strain 9FUST revealed 98.9% similarity of the 16S rRNA gene sequence with the closely related strain ‘Pseudodesulfovibrio methanolicus’ 5S69T and was studied in detail to enhance the taxonomic resolution. Strain 9FUST grew optimally at 23–28 °C, pH 6.5, and 0–2% (w/v) NaCl. The strain used lactate, pyruvate, methanol, ethanol, fructose, ribose, and H2/CO2 (in the presence of acetate) as carbon and energy sources for sulfate reduction. Iso-C17:1 ω11, C15:0, iso-C15:0, and C16:0 were the predominant fatty acids. The genome is 4.20 Mbp with a G + C content of 64.0%. The average nucleotide identity and digital DNA–DNA hybridization values with Pseudodesulfovibrio spp. genomes were 72.5–91.6% (&lt;95%) and 18.5–45.0% (&lt;70%), respectively, and supported our conclusion that 9FUST (=VKM B-3654T = KCTC 25498T) belonged to a novel Pseudodesulfovibrio species, for which the name Pseudodesulfovibrio karagichevae sp. nov. is proposed. Pangenome analysis of sixteen Pseudodesulfovibrio species and functional annotation analysis of identified genes revealed complete modules of enzymes of the main metabolic pathways, characteristic of bacteria of this genus, and unique genes highlighting the adaptations of strain 9FUST in carbohydrate metabolism, nutrient uptake, and environmental stress response. Isolation of these strains expands our understanding of the diversity of sulfidogens in oil reservoirs and can be used to test the effectiveness of biocides used in an oil field.

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• A new mesophilic member of the <i>Chloroflexota</i> phylum ‘<i>Ca</i>. Сhloroploca septentrionalis’ from the meromictic lake Bol'shie Khruslomeny separated from the White Sea

  FEMS Microbiology Letters · 2024-12-24

  articleOpen access

  A new filamentous phototrophic bacterium Khr17 was isolated as an enrichment culture from the brackish polar lake Bol'shie Khruslomeny. The organism was a halotolerant, strictly anaerobic phototroph possessing photosystem II. Sulfide was required for phototrophic growth. The cells of bacterium Khr17 formed nonmotile, wavy trichomes surrounded by a sheath. The cells contained chlorosomes, gas vesicles, and storage granules. The antenna pigments of bacterium Khr17 were bacteriochlorophyll c and β- and γ-carotenes. The genome of Khr17 bacterium carries all the genes responsible for CO2 fixation via the 3-hydroxypropionate pathway. The genes encoding the proteins of the nitrogenase complex were not found. The DNA G + C content was 59.9%. The 16S rRNA gene sequence of isolate Khr17 exhibited 99.4% similarity to related species. The average nucleotide identity and digital DNA-DNA hybridization values for the isolate showed 91.9% and 46.9% similarity, respectively, to other 'Ca. Chloroploca' species. Based on its phenotypic and phylogenetic characteristics, classification of Khr17 as member of a new species, 'Ca. Chloroploca septentrionalis' sp. nov., was proposed. Members of the genus 'Ca. Chloroploca' have previously not been found in Arctic areas and in the plankton of meromictic lakes.

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• Present Understanding of Biodiversity of Anoxygenic Phototrophic Bacteria in the Relic Lake Mogilnoe (Kildin Island, Murmansk Oblast, Russia)

  Microbiology · 2024-05-14 · 2 citations

  article

  The relic Lake Mogilnoe, separated from the Barents Sea by a sand and pebble dam, is located in the high Arctic on the Kildin island (Murmansk region). This lake is a classic example of a meromictic basin of marine origin. The data obtained during the 2018 expedition showed changes in the hydrochemical regime of the lake that have occurred over the past 20 years. Sulfide concentration in the monimolimnion of the lake was as high as 140 mg/L. A tendency for salinization of the surface waters to 7 g/L has been noted. The Lake Mogilnoe is characterized by a discrepancy between the halocline and thermocline levels. The chemocline zone in the lake is below the halocline level. In a narrow oxygen-containing layer between 3 and 7.5 m, aerobic microflora of the marine type and marine fauna were present. The bacterial plate was formed at the boundary of the sulfide layer at ~8 m and mainly consisted of green sulfur bacteria (GSB). Brown-colored GSB species containing bacteriochlorophyll e were predominant. The previously formed concept of anaerobic phototrophic bacteria (APB) biodiversity based on morphological characteristics was modified using metagenomic data obtained by analyzing DNA from two samples of lake water in the chemocline zone, and was also supplemented by identifying new GSB species. Molecular diagnostic data confirmed the absolute dominance of the brackish species of GSB Chlorobium phaeovibrioides. This is the first isolation and identification of brown- and green-colored Prosthecochloris aestuarii morphotypes from Lake Mogilnoe, as well as of bacteriochlorophyll c-containing Prosthecochloris sp. The taxonomic position of Pelodyction phaem, which was constantly present in the Lake Mogilnoe, is discussed in detail. Despite the partial isolation of the ecosystem of Lake Mogilnoe from the Barents Sea, the main properties of the dominant GSB species and Prosthecochlori aestuarii turned out to be similar to those of the phylotypes living in lakes on the White Sea coast.

  PublisherDOI

• Chromosome-level genome assembly of the bay scallop Argopecten irradians

  Scientific Data · 2024-09-28 · 5 citations

  articleOpen access1st authorCorresponding

  The bay scallop, Argopecten irradians, is a species of major commercial, cultural, and ecological importance. It is endemic to the eastern coast of the United States, but has also been introduced to China, where it supports a significant aquaculture industry. Here, we provide an annotated chromosome-level reference genome assembly for the bay scallop, assembled using PacBio and Hi-C data. The total genome size is 845.9 Mb, distributed over 1,503 scaffolds with a scaffold N50 of 44.3 Mb. The majority (92.9%) of the assembled genome is contained within the 16 largest scaffolds, corresponding to the 16 chromosomes confirmed by Hi-C analysis. The assembly also includes the complete mitochondrial genome. Approximately 36.2% of the genome consists of repetitive elements. The BUSCO analysis showed a completeness of 96.2%. We identified 33,772 protein-coding genes. This genome assembly will be a valuable resource for future research on evolutionary dynamics, adaptive mechanisms, and will support genome-assisted breeding, contributing to the conservation and management of this iconic species in the face of environmental and pathogenic challenges.

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• Erratum to: Prosthecodimorpha staleyi gen. nov., sp. nov., Novel Prosthecate Bacteria within the Family Ancalomicrobiaceae and Reclassification of the Polyphyletic Genus Prosthecomicrobium

  Microbiology · 2024-11-29 · 1 citations

  erratumOpen access

  An Erratum to this paper has been published: https://doi.org/10.1134/S0026261724607589

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Frequent coauthors

• Veronika Koziaeva

  Bioengineering Center

  41 shared

• Tamara N. Nazina

  Russian Academy of Sciences

  37 shared

• Maria Uzun

  Lomonosov Moscow State University

  34 shared

• Maria Krutkina

  26 shared

• Marina Dziuba

  University of Bayreuth

  23 shared

• Diyana S. Sokolova

  Russian Academy of Sciences

  23 shared

• А. Б. Полтараус

  Engelhardt Institute of Molecular Biology

  20 shared

• Б. Б. Кузнецов

  Russian Academy of Sciences

  20 shared

Labs

• Marine Animal Disease LaboratoryPI

Education

• PhD, Faculty of Biology

  Moskovskij gosudarstvennyj universitet imeni M V Lomonosova

  2014