Genomic and morphological characterization of a new Thiothrix species from a sulfide hot spring of the Zmeinaya bay (Northern Baikal, Russia).

A survey for bacteria of the genus Thiothrix indicated that they inhabited the area where the water of the Zmeiny geothermal spring (northern basin of Lake Baikal, Russia) mixed with the lake water. In the coastal zone of the lake oxygen (8.25 g/L) and hydrogen sulfide (up to 1 mg/L) were simultaneously present at sites of massive growth of these particular Thiothrix bacteria. Based on the analysis of the morphological characteristics and sequence of individual genes (16S rRNA, rpoB and tilS), we could not attribute the Thiothrix from Lake Baikal to any of the known species of this genus. To determine metabolic capabilities and phylogenetic position of the Thiothrix sp. from Lake Baikal, we analyzed their whole genome. Like all members of this genus, the bacteria from Lake Baikal were capable of organo-heterotrophic, chemolithoheterotrophic, and chemolithoautotrophic growth and differed from its closest relatives in the spectrum of nitrogen and sulfur cycle genes as well as in the indices of average nucleotide identity (ANI < 75-94%), amino acid identity (AAI < 94%) and in silico DNA-DNA hybridization (dDDH < 17-57%), which were below the boundary of interspecies differences, allowing us to identify them as novel candidate species.

Myxobolus nekrasovae n. sp. (Cnidaria, Myxozoa) is a new species parasitizing the gills of the gibel carp, Carassius auratus gibelio.

A new Myxobolus species, Myxobolus nekrasovi n. sp., was found in the gill arch of the gibel carp Carassius auratus gibelio during investigation of fish myxosporean fauna of ponds of Lake Baikal basin. The parasites were studied on the basis of spore morphology, as well as with histological and molecular methods. Mature spores of M. nekrasovi n. sp. are ellipsoidal in frontal view and lemon-shaped in lateral view, measuring 13.84 ± 0.4 (12.2-15) µm in length, 9.73 ± 0.2 (8.5-10.7) µm in width, 6,75 ± 0.1 (6.0-7.6) µm in thickness. Polar capsules are unequal and pyriform, measuring: length 6.31 ± 0.1 (5.4-7.4), width 3.49 ± 0.04 (3.12-4) µm and length 2.88 ± 0.1 (2.1-3.5), width 1.4 ± 0.03 (1-1.6) µm. Phylogenetic analysis with the SSU rDNA gene shows Myxobolus nekrasovae n. sp. as a sister species of the subclade formed by Thellohanellus sinensis, Myxobolus acutus, M. zhaltsanovae that infect gibel carp Carassius auratus gibelio.

Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal.

Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151T), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia. The new strain grows with molecular hydrogen as electron donor, elemental sulfur, and thiosulfate as electron acceptors, and CO2/[Formula: see text] as carbon source. The genome of strain PB12/4term consists of one chromosome with a total length of 2.820.915 bp and the G+C content of the genomic DNA was 72.2%. The phylogenomic reconstruction based on 120 conserved bacterial single-copy proteins revealed that strain PB12/4term belongs to the genus Thermaerobacter within in the class Thermaerobacteria, phylum Firmicutes_E. The strain PB12/4term is closely related to Thermaerobacter subterraneus DSM 13965 (ANI=95.08%, AF=0.91) and Thermaerobacter marianensis DSM 12885 (ANI=84.98%, AF=0.77). Genomic and experimental data confirm the ability of the Thermaerobacter PB12/4term pure culture to facultatively lithotrophic growth, which is provided by the presence of [NiFe]hydrogenase enzymes that are absent in T. marianensis DSM 12885 and T. subterraneus DSM 13965. The data obtained on the physiological and biochemical differences of strain PB12/4term provide a deeper insight into the species diversity and functional activity of the genus Thermaerobacter.

RNA-Seq Virus Fraction in Lake Baikal and Treated Wastewaters.

In this study, we analyzed the transcriptomes of RNA and DNA viruses from the oligotrophic water of Lake Baikal and the effluent from wastewater treatment plants (WWTPs) discharged into the lake from the towns of Severobaikalsk and Slyudyanka located on the lake shores. Given the uniqueness and importance of Lake Baikal, the issues of biodiversity conservation and the monitoring of potential virological hazards to hydrobionts and humans are important. Wastewater treatment plants discharge treated effluent directly into the lake. In this context, the identification and monitoring of allochthonous microorganisms entering the lake play an important role. Using high-throughput sequencing methods, we found that dsDNA-containing viruses of the class Caudoviricetes were the most abundant in all samples, while Leviviricetes (ssRNA(+) viruses) dominated the treated water samples. RNA viruses of the families Nodaviridae, Tombusviridae, Dicitroviridae, Picobirnaviridae, Botourmiaviridae, Marnaviridae, Solemoviridae, and Endornavirida were found in the pelagic zone of three lake basins. Complete or nearly complete genomes of RNA viruses belonging to such families as Dicistroviridae, Marnaviridae, Blumeviridae, Virgaviridae, Solspiviridae, Nodaviridae, and Fiersviridae and the unassigned genus Chimpavirus, as well as unclassified picorna-like viruses, were identified. In general, the data of sanitary/microbiological and genetic analyses showed that WWTPs inadequately purify the discharged water, but, at the same time, we did not observe viruses pathogenic to humans in the pelagic zone of the lake.

Viral Diversity in Samples of Freshwater Gastropods Benedictia baicalensis (Caenogastropoda: Benedictiidae) Revealed by Total RNA-Sequencing.

Previously, the main studies were focused on viruses that cause disease in commercial and farmed shellfish and cause damage to food enterprises (for example, Ostreavirusostreidmalaco1, Aurivirus haliotidmalaco1 and Aquabirnavirus tellinae). Advances in high-throughput sequencing technologies have extended the studies to natural populations of mollusks (and other invertebrates) as unexplored niches of viral diversity and possible sources of emerging diseases. These studies have revealed a huge diversity of mostly previously unknown viruses and filled gaps in the evolutionary history of viruses. In the present study, we estimated the viral diversity in samples of the Baikal endemic gastropod Benedictia baicalensis using metatranscriptomic analysis (total RNA-sequencing); we were able to identify a wide variety of RNA-containing viruses in four samples (pools) of mollusks collected at three stations of Lake Baikal. Most of the identified viral genomes (scaffolds) had only distant similarities to known viruses or (in most cases) to metagenome-assembled viral genomes from various natural samples (mollusks, crustaceans, insects and others) mainly from freshwater ecosystems. We were able to identify viruses similar to those previously identified in mollusks (in particular to the picornaviruses Biomphalaria virus 1 and Biomphalaria virus 3 from the freshwater gastropods); it is possible that picorna-like viruses (as well as a number of other identified viruses) are pathogenic for Baikal gastropods. Our results also suggested that Baikal mollusks, like other species, may bioaccumulate or serve as a reservoir for numerous viruses that infect a variety of organisms (including vertebrates).

Diversification along a benthic to pelagic gradient contributes to fish diversity in the world's largest lake (Lake Baikal, Russia).

Insights into the generation of diversity in both plants and animals have relied heavily on studying speciation in adaptive radiations. Russia's Lake Baikal has facilitated a putative adaptive radiation of cottid fishes (sculpins), some of which are highly specialized to inhabit novel niches created by the lake's unique geology and ecology. Here, we test evolutionary relationships and novel morphological adaptation in a piece of this radiation: the Baikal cottid genus, Cottocomephorus, a morphologically derived benthopelagic genus of three described species. We used a combination of mitochondrial DNA and restriction site associated DNA sequencing from all Cottocomephorus species. Analysis of mitochondrial cytochrome b haplotypes was only able to two resolve two lineages: C. grewingkii and C. comephoroides/inermis. Phylogenetic inference, principal component analysis, and faststructure of genome-wide SNPs uncovered three lineages within Cottocomephorus: C. comephoroides, C. inermis and C. grewingkii. We found recent divergence and admixture between C. comephoroides and C. inermis and deep divergence between these two species and C. grewingkii. Contrasting other fish radiations, we found no evidence of ancient hybridization among Cottocomephorus species. Digital morphology revealed highly derived pelagic phenotypes that reflect divergence by specialization to the benthopelagic niche in Cottocomephorus. Among Cottocomephorus species, we found evidence of ongoing adaptation to the pelagic zone. This pattern highlights the importance of speciation along a benthic-pelagic gradient seen in Cottocomephorus and across other adaptive fish radiations.

Anaerobic oxidation of petroleum hydrocarbons in enrichment cultures from sediments of the Gorevoy Utes natural oil seep under methanogenic and sulfate-reducing conditions.

This article presents the first experimental data on the ability of microbial communities from sediments of the Gorevoy Utes natural oil seep to degrade petroleum hydrocarbons under anaerobic conditions. Like in marine ecosystems associated with oil discharge, available electron acceptors, in particular sulfate ions, affect the composition of the microbial community and the degree of hydrocarbon conversion. The cultivation of the surface sediments under sulfate-reducing conditions led to the formation of a more diverse bacterial community and greater loss of n-alkanes (28%) in comparison to methanogenic conditions (6%). Microbial communities of both surface and deep sediments are more oriented to degrade polycyclic aromatic hydrocarbons (PAHs), to which the degree of the PAH conversion testifies (up to 46%) irrespective of the present electron acceptors. Microorganisms with the uncultured closest homologues from thermal habitats, sediments of mud volcanoes, and environments contaminated with hydrocarbons mainly represented microbial communities of enrichment cultures. The members of the phyla Firmicutes, Chloroflexi, and Caldiserica (OP5), as well as the class Deltaproteobacteria and Methanomicrobia, were mostly found in enrichment cultures. The influence of gas-saturated fluids may be responsible for the presence in the bacterial 16S rRNA gene libraries of the sequences of "rare taxa": Planctomycetes, Ca. Atribacteria (OP9), Ca. Armatimonadetes (OP10), Ca. Latescibacteria (WS3), Ca. division (AC1), Ca. division (OP11), and Ca. Parcubacteria (OD1), which can be involved in hydrocarbon oxidation.

Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal.

Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.

Unique and ancestral features in trunk kidney microanatomy and ultrastructure of omul Coregonus migratorius.

This study presents novel data on the microanatomy and ultrastructure of the omul Coregonus migratorius trunk kidney. Adult individuals of C. migratorius were sampled in the Barguzin Bay of Lake Baikal. Active leuko- and erythropoiesis were found in the interstitium of the mesonephros. For the first time, cells with radially arranged vesicles have been described in the renal interstitium of C. migratorius. The quantitative characteristics of blood cells and ultrastructural parameters of leukocytes reflected the functioning of the non-specific defence system in the organism. The share of the renal interstitium, morphological diversity of the epithelial cells of the nephron tubules, the ultrastructural features of the renal corpuscles and nephron tubules and the number of mitochondria in leukocytes and ion-transporting cells were typical for representatives of the whitefish Coregonus lavaretus complex and thus considered ancestral features of the present-day C. migratorius population reflecting its adaptive potential to living in an ultra-deep Lake Baikal.

Different ways to play it cool: Transcriptomic analysis sheds light on different activity patterns of three amphipod species under long-term cold exposure.

Species of littoral freshwater environments in regions with continental climate experience pronounced seasonal temperature changes. Coping with long cold winters and hot summers requires specific physiological and behavioural adaptations. Endemic amphipods of Lake Baikal, Eulimnogammarus verrucosus and Eulimnogammarus cyaneus, show high metabolic activity throughout the year; E. verrucosus even reproduces in winter. In contrast, the widespread Holarctic amphipod Gammarus lacustris overwinters in torpor. This study investigated the transcriptomic hallmarks of E. verrucosus, E. cyaneus and G. lacustris exposed to low water temperatures. Amphipods were exposed to 1.5°C and 12°C (corresponding to the mean winter and summer water temperatures, respectively, in the Baikal littoral) for one month. At 1.5°C, G. lacustris showed upregulation of ribosome biogenesis and mRNA processing genes, as well as downregulation of genes related to growth, reproduction and locomotor activity, indicating enhanced energy allocation to somatic maintenance. Our results suggest that the mitogen-activated protein kinase (MAPK) signalling pathway is involved in the preparation for hibernation; downregulation of the actin cytoskeleton pathway genes could relate to the observed low locomotor activity of G. lacustris at 1.5°C. The differences between the transcriptomes of E. verrucosus and E. cyaneus from the 1.5°C and 12°C exposures were considerably smaller than for G. lacustris. In E. verrucosus, cold-exposure triggered reproductive activity was indicated by upregulation of respective genes, whereas in E. cyaneus, genes related to mitochondria functioning were upregulated, indicating cold compensation in this species. Our data elucidate the molecular characteristics behind the different adaptations of amphipod species from the Lake Baikal area to winter conditions.

Environmental Monitoring of the Littoral Zone of Lake Baikal Using a Network of Automatic Hydro-Meteorological Stations: Development and Trial Run.

An automatic hydro-meteorological station (AHMS) was designed to monitor the littoral zone of Lake Baikal in areas with high anthropogenic pressure. The developed AHMS was installed near the Bolshiye Koty settlement (southern basin). This AHMS is the first experience focused on obtaining the necessary competencies for the development of a monitoring network of the Baikal natural territory. To increase the flexibility of adjustment and repeatability, we developed AHMS as a low-cost modular system. AHMS is equipped with a weather station and sensors measuring water temperature, pH, dissolved oxygen, redox potential, conductivity, chlorophyll-a, and turbidity. This article describes the main AHMS functions (hardware and software) and measures taken to ensure data quality control. We present the results of the first two periods of its operation. The data acquired during this periods have demonstrated that, to obtain accurate measurements and to detect and correct errors that were mainly due to biofouling of the sensors and calibration bias, a correlation between AHMS and laboratory studies is necessary for parameters such as pH and chlorophyll-a. The gained experience should become the basis for the further development of the monitoring network of the Baikal natural territory.

Autonomous System for Lake Ice Monitoring.

Continuous monitoring of ice cover belongs to the key tasks of modern climate research, providing up-to-date information on climate change in cold regions. While a strong advance in ice monitoring worldwide has been provided by the recent development of remote sensing methods, quantification of seasonal ice cover is impossible without on-site autonomous measurements of the mass and heat budget. In the present study, we propose an autonomous monitoring system for continuous in situ measuring of vertical temperature distribution in the near-ice air, the ice strata and the under-ice water layer for several months with simultaneous records of solar radiation incoming at the lake surface and passing through the snow and ice covers as well as snow and ice thicknesses. The use of modern miniature analog and digital sensors made it possible to make a compact, energy efficient measurement system with high precision and spatial resolution and characterized by easy deployment and transportation. In particular, the high resolution of the ice thickness probe of 0.05 mm allows to resolve the fine-scale processes occurring in low-flow environments, such as freshwater lakes. Several systems were tested in numerous studies in Lake Baikal and demonstrated a high reliability in deriving the ice heat balance components during ice-covered periods.

Long-term cyclicity of trace element in the Baikal aquatic ecosystem (Russia).

Longitudinal monitoring studies (between 2006 and 2019) of the chemical composition of the water from the Angara River source (the runoff of Lake Baikal) revealed the interannual, year-round and monthly cyclicity in the distribution of some trace elements vis-à-vis their concentrations. The change in the concentrations of elements was contingent on the season, the temperature of the air and water, the activity of phyto- and zooplankton and regional changes in the environment (floods, earthquakes, fires, tourism, ships, technogenesis etc.). We compared the concentrations of trace elements present in the water samples from the Angara source and the water samples from Lake Baikal with the maximum permissible concentration values for drinking water. The calculated (median) concentrations for water samples from the Angara source, which spanned the entire study period, were close to the data obtained for the Baikal water.

Symbiosis, Selection, and Novelty: Freshwater Adaptation in the Unique Sponges of Lake Baikal.

Freshwater sponges (Spongillida) are a unique lineage of demosponges that secondarily colonized lakes and rivers and are now found ubiquitously in these ecosystems. They developed specific adaptations to freshwater systems, including the ability to survive extreme thermal ranges, long-lasting dessication, anoxia, and resistance to a variety of pollutants. Although spongillids have colonized all freshwater systems, the family Lubomirskiidae is endemic to Lake Baikal and plays a range of key roles in this ecosystem. Our work compares the genomic content and microbiome of individuals of three species of the Lubomirskiidae, providing hypotheses for how molecular evolution has allowed them to adapt to their unique environments. We have sequenced deep (>92% of the metazoan "Benchmarking Universal Single-Copy Orthologs" [BUSCO] set) transcriptomes from three species of Lubomirskiidae and a draft genome resource for Lubomirskia baikalensis. We note Baikal sponges contain unicellular algal and bacterial symbionts, as well as the dinoflagellate Gyrodinium. We investigated molecular evolution, gene duplication, and novelty in freshwater sponges compared with marine lineages. Sixty one orthogroups have consilient evidence of positive selection. Transporters (e.g., zinc transporter-2), transcription factors (aristaless-related homeobox), and structural proteins (e.g. actin-3), alongside other genes, are under strong evolutionary pressure in freshwater, with duplication driving novelty across the Spongillida, but especially in the Lubomirskiidae. This addition to knowledge of freshwater sponge genetics provides a range of tools for understanding the molecular biology and, in the future, the ecology (e.g., colonization and migration patterns) of these key species.

Morphological, histological, and molecular aspects of Myxobolus zaikae n. sp., a parasite of the roach Rutilus rutilus, in Lake Baikal.

A new myxobolid species, Myxobolus zaikae n. sp., was found in the connective tissue near the kidney and liver blood vessels of the common roach Rutilus rutilus, while fish myxosporean fauna were being investigated in Lake Baikal, Russia. The parasites were studied on the basis of spore morphology as well as with histological and molecular methods. Mature spores of M. zaikae n. sp. are round or ellipsoidal in the frontal view and lemon-shaped in the lateral view, measuring 11.37 ± 0.11 µm (10.2-14.0 µm) in length, 10.29 ± 0.10 µm (9.6-11.0 µm) in width, and 6.3 ± 0.08 µm (5.8-7.1 µm) in thickness (mean ± SD; n = 50). Polar capsules are equal and pyriform, measuring 4.5 ± 0.07 µm (3.4-5.2 µm) in length and 2.9 ± 0.03 µm (2.6-3.3 µm) in width. Polar capsules contained polar filaments coiled with 5 to 6 turns. Phylogenetic analysis showed that this newly described species clusters with other myxobolid species infecting the connective tissue of different organs from Palearctic cyprinid fish.

Bacterial Communities in Areas of Oil and Methane Seeps in Pelagic of Lake Baikal.

We have assessed the diversity of bacteria near oil-methane (area I) and methane (area II) seeps in the pelagic zone of Lake Baikal using massive parallel sequencing of 16S rRNA, pmoA, and mxaF gene fragments amplified from total DNA. At depths from the surface to 100 m, sequences belonging to Cyanobacteria dominated. In the communities to a depth of 200 m of the studied areas, Proteobacteria dominated the deeper layers of the water column. Alphaproteobacteria sequences were predominant in the community near the oil-methane seep, while the community near the methane seep was characterized by the prevalence of Alpha- and Gammaproteobacteria. Among representatives of these classes, type I methanotrophs prevailed in the 16S rRNA gene libraries from the near-bottom area, and type II methanotrophs were detected in minor quantities at different depths. In the analysis of the libraries of the pmoA and mxaF functional genes, we observed the different taxonomic composition of methanotrophic bacteria in the surface and deep layers of the water column. All pmoA sequences from area I were type II methanotrophs and were detected at a depth of 300 m, while sequences of type I methanotrophs were the most abundant in deep layers of the water column of area II. All mxaF gene sequences belonged to Methylobacterium representatives. Based on comparative analyses of 16S rRNA, pmoA, and mxaF gene fragment libraries, we suggest that there must be a wider spectrum of functional genes facilitating methane oxidation that were not detected with the primers used.

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom.

The pelagic zone of Lake Baikal is an ecological niche where phytoplankton bloom causes increasing microbial abundance in spring which plays a key role in carbon turnover in the freshwater lake. Co-occurrence patterns revealed among different microbes can be applied to predict interactions between the microbes and environmental conditions in the ecosystem. We used 454 pyrosequencing of 16S rRNA and 18S rRNA genes to study bacterial and microbial eukaryotic communities and their co-occurrence patterns at the pelagic zone of Lake Baikal during a spring phytoplankton bloom. We found that microbes within one domain mostly correlated positively with each other and are highly interconnected. The highly connected taxa in co-occurrence networks were operational taxonomic units (OTUs) of Actinobacteria, Bacteroidetes, Alphaproteobacteria, and autotrophic and unclassified Eukaryota which might be analogous to microbial keystone taxa. Constrained correspondence analysis revealed the relationships of bacterial and microbial eukaryotic communities with geographical location.

The cyclicity in the changes in the chemical composition of the water source of the Angara River (Baikal Stock) in 2017-2018 in comparison with the last 20 years of data.

The relevance of the research is due to the increasing need for drinking water in the world, the shortage of which is experienced in many countries. The main aim is the study of the chemical composition of freshwater of the Angara River (the drain of Lake Baikal) and the characteristics of its changes. Methods of research: water was sampled at a distance of 1.5-2 m from the shore, from a depth of 0.4-0.5 m, and at the source water intake with the help of a pump. Samples were taken in clean plastic bottles of 1 L in size to determine SO42-, Cl-, HCO3-, NO2-, HNO3-, SiO2, F-, PO43-, NH4+, O2, EC, EH, Ca2+, Mg2+, Na+, K+, pH, and temperature. The analyses were accomplished according to standard techniques. It is shown that minor changes in the total content of ions in the water of the Angara River source occur daily, monthly, and depend on a season. Graphically, this is expressed by the curve (broken) line, which manifested the increase, maximum, decrease, minimum, and eventually an endless cycle of repeating the sequence of monthly and annual concentrations of the elements. It was found that the average values of the main ions in the water and the total mineralization of the water source of Angara River and Lake Baikal correspond to their average annual values over the past 20 years. The reason for the constant chemical composition of Baikal and Angara waters may be not only the possibility of already proven chemical and biological self-purification but also the additional penetration of deep waters as a result of upwelling and earthquakes on Lake Baikal. It is concluded that it is necessary to continue further geochemical and microbiological monitoring of the Baikal aquatic ecosystem to assess its composition and quality.

Genomes of Novel Microbial Lineages Assembled from the Sub-Ice Waters of Lake Baikal.

We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep sequenced and the reads assembled to generate metagenome-assembled genomes (MAGs) that are representative of the microbes living in this special environment. Compared with freshwater bodies studied around the world, Lake Baikal had an unusually high fraction of Verrucomicrobia Other groups, such as Actinobacteria and Proteobacteria, were in proportions similar to those found in other lakes. The genomes (and probably cells) tended to be small, presumably reflecting the extremely oligotrophic and cold prevalent conditions. Baikal microbes are novel lineages recruiting very little from other water bodies and are distantly related to other freshwater microbes. Despite their novelty, they showed the closest relationship to genomes discovered by similar approaches from other freshwater lakes and reservoirs. Some of them were particularly similar to MAGs from the Baltic Sea, which, although it is brackish, connected to the ocean, and much more eutrophic, has similar climatological conditions. Many of the microbes contained rhodopsin genes, indicating that, in spite of the decreased light penetration allowed by the thick ice/snow cover, photoheterotrophy could be widespread in the water column, either because enough light penetrates or because the microbes are already adapted to the summer ice-less conditions. We have found a freshwater SAR11 subtype I/II representative showing striking synteny with Pelagibacterubique strains, as well as a phage infecting the widespread freshwater bacterium PolynucleobacterIMPORTANCE Despite the increasing number of metagenomic studies on different freshwater bodies, there is still a missing component in oligotrophic cold lakes suffering from long seasonal frozen cycles. Here, we describe microbial genomes from metagenomic assemblies that appear in the upper water column of Lake Baikal, the largest and deepest freshwater body on Earth. This lake is frozen from January to May, which generates conditions that include an inverted temperature gradient (colder up), decrease in light penetration due to ice, and, especially, snow cover, and oligotrophic conditions more similar to the open-ocean and high-altitude lakes than to other freshwater or brackish systems. As could be expected, most reconstructed genomes are novel lineages distantly related to others in cold environments, like the Baltic Sea and other freshwater lakes. Among them, there was a broad set of streamlined microbes with small genomes/intergenic spacers, including a new nonmarine Pelagibacter-like (subtype I/II) genome.

Epilithic Biofilms in Lake Baikal: Screening and Diversity of PKS and NRPS Genes in the Genomes of Heterotrophic Bacteria.

A collection of heterotrophic bacteria consisting of 167 strains was obtained from microbial communities of biofilms formed on solid substrates in the littoral zone of Lake Baikal. Based on the analysis of 16S rRNA gene fragments, the isolates were classified to four phyla: Proteobacteria , Firmicutes , Actinobacteria , and Bacteroidetes . To assess their biotechnological potential, bacteria were screened for the presence of PKS (polyketide synthase) and NRPS (non-ribosomal peptide synthetases) genes. PKS genes were detected in 41 strains (25%) and NRPS genes in 73 (43%) strains by PCR analysis. The occurrence of PKS genes in members of the phylum Firmicutes (the genera Bacillus and Paenibacillus ) was 34% and NRPS genes were found in 78%. In Proteobacteria , PKS and NRPS genes were found in 20% and 32%, and in 22% and 22% of Actinobacteria , respectively. For further analysis of PKS and NRPS genes, six Bacillus and Paenibacillus strains with antagonistic activity were selected and underwent phylogenetic analysis of 16S rRNA genes. The identification of PKS and NRPS genes in the strains investigated was demonstrated among the homologues the genes involved in the biosynthesis of antibiotics (bacillaene, difficidine, erythromycin, bacitracin, tridecaptin, and fusaricidin), biosurfactants (iturin, bacillomycin, plipastatin, fengycin, and surfactin) and antitumor agents (epothilone, calyculin, and briostatin). Bacillus spp. 9A and 2A strains showed the highest diversity of PKS and NRPS genes. Bacillus and Paenibacillus strains isolated from epilithic biofilms in Lake Baikal are potential producers of antimicrobial compounds and may be of practical interest for biotechnological purposes.A collection of heterotrophic bacteria consisting of 167 strains was obtained from microbial communities of biofilms formed on solid substrates in the littoral zone of Lake Baikal. Based on the analysis of 16S rRNA gene fragments, the isolates were classified to four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. To assess their biotechnological potential, bacteria were screened for the presence of PKS (polyketide synthase) and NRPS (non-ribosomal peptide synthetases) genes. PKS genes were detected in 41 strains (25%) and NRPS genes in 73 (43%) strains by PCR analysis. The occurrence of PKS genes in members of the phylum Firmicutes (the genera Bacillus and Paenibacillus) was 34% and NRPS genes were found in 78%. In Proteobacteria, PKS and NRPS genes were found in 20% and 32%, and in 22% and 22% of Actinobacteria, respectively. For further analysis of PKS and NRPS genes, six Bacillus and Paenibacillus strains with antagonistic activity were selected and underwent phylogenetic analysis of 16S rRNA genes. The identification of PKS and NRPS genes in the strains investigated was demonstrated among the homologues the genes involved in the biosynthesis of antibiotics (bacillaene, difficidine, erythromycin, bacitracin, tridecaptin, and fusaricidin), biosurfactants (iturin, bacillomycin, plipastatin, fengycin, and surfactin) and antitumor agents (epothilone, calyculin, and briostatin). Bacillus spp. 9A and 2A strains showed the highest diversity of PKS and NRPS genes. Bacillus and Paenibacillus strains isolated from epilithic biofilms in Lake Baikal are potential producers of antimicrobial compounds and may be of practical interest for biotechnological purposes.