Aquatic Science, Ecology, Evolution, Behavior and Systematics, Ecology, Nature and Landscape Conservation
29
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389
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12
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12
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Scopus Publications
Efficient recovery and DNA extraction for algae-associated microbial communities Elizaveta Chevokina, Daria Sibiryakina, Andrey Sobolev, Darya Slonova, Alina Demkina, et al. Frontiers in Plant Science, 2026 The extraction of high-quality microbial DNA from environmental samples is critical for many downstream applications, including short- and long-read metagenomic sequencing. However, environmental DNA is prone to low recovery, degradation, and contamination by enzymatic inhibitors, with the extent of these issues largely dependent on the DNA purification method. The embedding of bacterial cells in a mucoid matrix within biofilms further complicates the process, making the study of algal symbionts particularly challenging. This study benchmarked five methods to recover microbial cells from biofilms associated with three major groups of marine macroalgae, namely: red ( Palmaria stenogona ), brown ( Saccharina japonica ), and green ( Ulva lactuca ). This was followed by a systematic evaluation of six widely used commercial DNA purification kits for their ability to extract high-quality DNA suitable for 16S rRNA gene and shotgun sequencing. A universal trade-off was observed between the quantity and quality of the extracted DNA. While whole-sample homogenization and manual collection of biofilms resulted in high levels of chloroplast contamination, washing microbial cells with a buffer led to low DNA recovery; however, the use of a detergent improved DNA yields. A comparison of the DNA extraction kits revealed that their efficiency varied significantly among algal species, with the GeneJET Genomic DNA Purification Kit (Thermo Scientific) identified as the most versatile. The present findings provide a comparative benchmark of methods to recover algae-associated microbial communities and extract their DNA, offering guidance in selecting procedures suited for metagenomic sequencing.
Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples Andrey Sobolev, Daria Sibiryakina, Elizaveta Chevokina, Darya Slonova, Daria Yurikova, et al. International Journal of Molecular Sciences, 2025 Extraction of high-quality microbial DNA remains a critical bottleneck in metagenomic research. Environmental samples often produce fragmented DNA and are prone to contaminations that interfere with downstream sequencing, while widely used commercial kits can be prohibitively expensive. Therefore, systematic evaluation of cost-effective alternatives is essential to support large-scale metagenomic studies. In this work, we benchmarked eight commercial DNA extraction kits from Magen, SkyGen, and Sileks against Qiagen reference kits. Four representative sample types were analyzed: freshwater, seafloor sediments, Pacific oyster (Magallana gigas) gut microbiome, and mammalian feces. DNA yield, integrity, purity, PCR inhibitor content, and eukaryotic DNA admixture were assessed. Microbial community composition, alpha diversity, reproducibility, and contamination (“kitome” and “splashome”) were further evaluated using 16S rRNA amplicon sequencing. We revealed that several alternative kits performed comparably or better than the Qiagen reference standard. Magen Soil and Magen Bacterial provided high yields and reproducibility, though the latter produced more fragmented DNA. SkyGen Stool excelled with host-associated samples, while Sileks Soil and Metagenomic kits preserved higher diversity in sediments. Magen Microbiome consistently underperformed. This study identifies multiple cost-effective DNA extraction strategies and provides practical guidance for selecting balanced DNA purification methods for different sample types.
Sea ice decline in the Eastern Arctic results in expansion of the freshened surface layer Vladimir Rogozhin, Alexander Osadchiev, Alexander Savin, Ekaterina Rogozhina, Anton Georgiev, et al. Frontiers in Marine Science, 2025 In this study, we report an anomalously large freshened surface layer in the Eastern Arctic during ice-free season in 2019. This freshened surface layer is formed by river discharge and sea ice meltwater and is also referred to as the Lena plume, due to the Lena River discharge is its major freshwater source. Based on in situ and satellite data, we demonstrate that in August-September 2019 the Lena plume extended from the Lena Delta in the west to the Wrangel Island in the east, i.e., its zonal extent was approximately 2000 km. The area of the Lena plume varied between 750 000 and 870 000 km2 during this period, which is 1.5 times greater than the assessment of its maximal area in previous years, albeit they were often hindered by the presence of sea ice coverage. The main reasons for this anomalous spreading of the Lena plume are the following. First, intense sea ice melting in the Eastern Arctic in 2019 provided a significantly greater volume of meltwater inflow to the freshened surface layer, as compared to other years. Second, sea ice cleared out of the Laptev and East Siberian seas by the beginning of August and September 2019 respectively, and these seas remained free of ice during for 2 to 3 months (longer ice-free period occurred only in 2007 and 2020). Three months of favorable wind forcing on the Lena plume in July-September 2019 caused its anomalously extensive eastward and northward expansion, together with changes in the vertical structure of the Lena plume. This plume expansion affected the composition of phytoplankton communities, with the intrusion of freshwater species in the eastern part of the East Siberian Sea. The reported expansion of the large Lena plume under favorable sea ice and wind conditions provides the baseline for forecasting the future state of large-scale freshwater cycle in the Arctic Ocean, with an expectedly reduced ice cover.
Benthic communities under methane gradient in the Laptev and East Siberian seas Olga Konovalova, Nadezhda Rimskaya-Korsakova, Petr Kuznetsov, Alexander Osadchiev, Maria Fedyaeva, et al. Frontiers in Ecology and Evolution, 2024 IntroductionMethane seeps influence surrounding benthic communities in different ways from slight changes in benthic abundance and biomass to major altering the species composition.Materials and MethodsWe studied benthic communities of 14 methane seep flares in Laptev and East Siberian seas with comparative analysis of species composition and abiotic parameters at the nearby areas not affected by methane seeps. The species diversity was comparable at seep and non-seep sites varying from 3.9 to 39.6 taxa per 100 individuals and from 4.5 to 34.8 taxa per 100 individuals, correspondingly.ResultsThe Laptev Slope community corresponds with the Polychaeta-community, encircling the upper continental slope area of the entire Siberian Arctic. The Lower Shelf community described in this study apparently corresponds with the Ophiocten sericeum community identified in the shelf areas of the Kara, Laptev and East Siberian seas. The Upper Shelf community is mostly inhabited by the bivalves species such as Portlandia arctica, Ennucula tenuis and Astarte montagui communities. The Estuarine community, which is the poorest by diversity but has high values of abundance and biomass is directly influenced by the Lena River runoff in terms of lower salinities and higher sedimentation rates.DiscussionThroughout the study area, the differences between the Estuarine, Upper Shelf, Lower Shelf and Laptev Slope communities exceeded the differences between the seep and background non-seep areas. Several taxa demonstrated correlations with different environmental factors, including the latitude, depth, temperature, salinity, pH and methane content, not depending on the revealed benthic community. Eight taxa demonstrated correlations with the methane content measured at different sediment depths. Two siboglinids taxa demonstrated high abundances at stations with highest methane content deep in the sediment. At the Siberian shelf, our geochemical data for siboglinid habitats are the first to be published so far.
Benchmarking DNA isolation methods for marine metagenomics Alina Demkina, Darya Slonova, Viktor Mamontov, Olga Konovalova, Daria Yurikova, et al. Scientific Reports, 2023 Metagenomics is a powerful tool to study marine microbial communities. However, obtaining high-quality environmental DNA suitable for downstream sequencing applications is a challenging task. The quality and quantity of isolated DNA heavily depend on the choice of purification procedure and the type of sample. Selection of an appropriate DNA isolation method for a new type of material often entails a lengthy trial and error process. Further, each DNA purification approach introduces biases and thus affects the composition of the studied community. To account for these problems and biases, we systematically investigated efficiency of DNA purification from three types of samples (water, sea sediment, and digestive tract of a model invertebrate Magallana gigas) with eight commercially available DNA isolation kits. For each kit-sample combination we measured the quantity of purified DNA, extent of DNA fragmentation, the presence of PCR-inhibiting contaminants, admixture of eukaryotic DNA, alpha-diversity, and reproducibility of the resulting community composition based on 16S rRNA amplicons sequencing. Additionally, we determined a “kitome”, e.g., a set of contaminating taxa inherent for each type of purification kit used. The resulting matrix of evaluated parameters allows one to select the best DNA purification procedure for a given type of sample.
Opportunistic consumption of marine pelagic, terrestrial, and chemosynthetic organic matter by macrofauna on the Arctic shelf: a stable isotope approach Valentin Kokarev, Anna K. Zalota, Andrey Zuev, Alexei Tiunov, Petr Kuznetsov, et al. Peerj, 2023 Macrofauna can contribute substantially to the organic matter cycling on the seafloor, yet the role of terrestrial and chemosynthetic organic matter in the diets of microphagous (deposit and suspension) feeders is poorly understood. In the present study, we used stable isotopes of carbon and nitrogen to test the hypothesis that the terrestrial organic matter supplied with river runoff and local chemosynthetic production at methane seeps might be important organic matter sources for macrofaunal consumers on the Laptev Sea shelf. We sampled locations from three habitats with the presumed differences in organic matter supply: “Delta” with terrestrial inputs from the Lena River, “Background” on the northern part of the shelf with pelagic production as the main organic matter source, and “Seep” in the areas with detected methane seepage, where chemosynthetic production might be available. Macrobenthic communities inhabiting each of the habitats were characterized by a distinct isotopic niche, mostly in terms of δ13C values, directly reflecting differences in the origin of organic matter supply, while δ15N values mostly reflected the feeding group (surface deposit/suspension feeders, subsurface deposit feeders, and carnivores). We conclude that both terrestrial and chemosynthetic organic matter sources might be substitutes for pelagic primary production in the benthic food webs on the largely oligotrophic Laptev Sea shelf. Furthermore, species-specific differences in the isotopic niches of species belonging to the same feeding group are discussed, as well as the isotopic niches of the symbiotrophic tubeworm Oligobrachia sp. and the rissoid gastropod Frigidoalvania sp., which are exclusively associated with methane seeps.
Structure and variability of the Pechora plume in the southeastern part of the Barents Sea Vladimir Rogozhin, Alexander Osadchiev, Olga Konovalova Frontiers in Marine Science, 2023 The Pechora River forms the large Pechora River plume in the southeastern part of the Barents Sea (also called the Pechora Sea). Many previous works addressed water masses in the Barents Sea, however, the Pechora plume received relatively little attention, therefore, many basic aspects of its structure and variability remain unknown. In this study, we focus on spreading of the Pechora plume in the Pechora Sea during ice-free periods. Based on the extensive in situ measurements and satellite observations, we describe the dependence of area and spatial characteristics of the Pechora plume on wind forcing, river discharge rate, and spring ice conditions. We reveal three general types of Pechora plume spreading, which are determined by the external forcing conditions. Joint analysis of a large set of in situ and satellite data provided opportunity to study the variability of the Pechora plume on the synoptic, seasonal, and interannual time scales. We reveal regular advection of the Pechora plume through the Kara Strait into the Kara Sea. In addition, we describe formation of a significant area of increased salinity within the Pechora plume formed during wind-induced coastal upwelling events. The results of this research are of key importance for understanding the physical, biological, and geochemical processes in the Pechora Sea and the adjacent areas of the Barents and Kara seas.
Production of Fluorescent Dissolved Organic Matter by Microalgae Strains from the Ob and Yenisei Gulfs (Siberia) Nikolay V. Lobus, Anton M. Glushchenko, Alexander A. Osadchiev, Yevhen I. Maltsev, Dmitry A. Kapustin, et al. Plants, 2022 Dissolved organic matter (DOM) is an important component of aquatic environments; it plays a key role in the biogeochemical cycles of many chemical elements. Using excitation–emission matrix fluorescence spectroscopy, we examined the fluorescent fraction of DOM (FDOM) produced at the stationary phase of growth of five strains of microalgae sampled and isolated from the Ob and Yenisei gulfs. Based on the morphological and molecular descriptions, the strains were identified as diatoms (Asterionella formosa, Fragilaria cf. crotonensis, and Stephanodiscus hantzschii), green microalgae (Desmodesmus armatus), and yellow-green microalgae (Tribonema cf. minus). Three fluorescent components were validated in parallel factor analysis (PARAFAC): one of them was characterized by protein-like fluorescence (similar to peak T), two others, by humic-like fluorescence (peaks A and C). The portion of fluorescence intensity of humic compounds (peak A) to the total fluorescence intensity was the lowest (27 ± 5%) and showed little variation between species. Protein-like fluorescence was most intense (45 ± 16%), but along with humic-like fluorescence with emission maximum at 470 nm (28 ± 14%), varied considerably for different algae strains. The direct optical investigation of FDOM produced during the cultivation of the studied algae strains confirms the possibility of autochthonous production of humic-like FDOM in the Arctic shelf regions.
Biology of stigmidium ascophylli - Fungal symbiont of fucoids in kandalaksha bay, white sea Mikologiya I Fitopatologiya, 2012
Fungi on brown seaweeds ascophyllum nodosum and pelvetia canaliculata in the kandalaksha bay of white sea Mikologiya I Fitopatologiya, 2011
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