Microorganisms of Lake Baikal : the deepest and most ancient lake on Earth

Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter. The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments

Additional file 1 of A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics [Dataset]

Additional file 1: Table S1. Summary statistics of the Baikal 1600 m long-read sequencing and metagenomic assembly. Fig. S1. A Principal component analysis (PCA) between deep Lake Baikal metagenomes based on a Bray-Curtis similarity k-mer profile frequencies of sequencing reads. Red and blue dots represent summer and winter Illumina metagenomes, respectively, while the green dot is the sample retrieved in this study and sequenced with PacBio Sequel II. B Phylum-level composition based on 16S rRNA gene fragments (Illumina and PacBio CCS5 reads) of the different metagenomes. The single metagenome highlighted in green corresponds to the PacBio sequencing, whilst the rest of datasets belong to previous Illumina sequencing. The phylum Proteobacteria was divided into its class-level classification. Only those groups with abundance values larger than 1% in any of the metagenomes are shown. C Classification of the 1600 m PacBio CCS5 16S rRNA reads at a higher taxonomic resolution. Only sequences larger than 1000 nucleotides were considered. Sequences ascribed to the Ca. Patescibacteria phylum are highlighted in green. Table S2. Genomic parameters of LAGs recovered in this study. Table S3. Genomic parameters of LAGs recovered in this study with ANI > 99.5% to MAGs retrieved from Lake Baikal 1250 and 1350 m deep. Fig. S2. Alignment of two LAGs that are complete in a single contig and the respective MAG from the Illumina assembly. Table S4. Genomic parameters of the resulting bins from the Baikal 1600 m CCS sequences. The four Baikalibacteria bins are highlighted in yellow. Fig. S3. A Maximum likelihood phylogenetic tree of the Baikalibacteria 16S rRNA genes. Sequences outside the deep branch coming from Figure 1 were used as an outgroup for the tree. The reads from the four read bins are colored in the figure. B Diversity of 16S rRNA sequences of Baikalibacteria bins. Linear representation of selected CCS5 reads (indicated with a red circle in the left panel) containing a 16S rRNA gene. A pairwise blastn comparison among reads was performed to detect orthologous genes. Fig. S4. A Average nucleotide identity based on metagenomic reads (ANIr) of LAGs and the four Baikalibacteria Bins. B ANIr of ten randomly selected sequences of each Baikalibacteria bin. Fig. S5. Metagenomic recruitment of the largest fragment of Baikalibacteria RBin09 on Lake Thun 180 m deep. Fig. S6. Maximum likelihood phylogenetic tree of the a phytoene elongase (LyeJ), b carotenoid 3,4-desaturase (CrtD), and c bisanhydrobacterioruberin hydratase (CruF) proteins.Peer reviewe

A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics

Background Lake Baikal, the world's deepest freshwater lake, contains important numbers of Candidatus Patescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating the potential of other groups being present. Here, we have applied for the first time a long-read (PacBio CCS) metagenomic approach to analyze in depth the Ca. Patescibacteria living in the bathypelagic water column of Lake Baikal at 1600 m. Results The retrieval of nearly complete 16S rRNA genes before assembly has allowed us to detect the presence of a novel and a likely endemic group of Ca. Patescibacteria inhabiting bathypelagic Lake Baikal. This novel group seems to possess extremely high intra-clade diversity, precluding complete genomes' assembly. However, read binning and scaffolding indicate that these microbes are similar to other Ca. Patescibacteria (i.e. parasites or symbionts), although they seem to carry more anabolic pathways, likely reflecting the extremely oligotrophic habitat they inhabit. The novel bins have not been found anywhere, but one of the groups appears in small amounts in an oligotrophic and deep alpine Lake Thun. We propose this novel group be named Baikalibacteria. Conclusion The recovery of 16S rRNA genes via long-read metagenomics plus the use of long-read binning to uncover highly diverse "hidden" groups of prokaryotes are key strategies to move forward in ecogenomic microbiology. The novel group possesses enormous intraclade diversity akin to what happens with Ca. Patescibacteria at the interclade level, which is remarkable in an environment that has changed little in the last 25 million yearsFunding: This work was supported by grants “VIREVO” CGL2016-76273-P [AEI/FEDER, EU], and “FLEX3GEN” PID2020-118052 GB-I00 (cofounded with FEDER funds) from the Spanish Ministerio de Economia, Industria y Competitividad, and “HIDRAS3” PROMETEU/2019/009 from Generalitat Valenciana to FR-V. JMH-M was supported with a PhD fellowship from Margarita Salas program, cofounded by the Spanish Ministerio de Universidades and the European Union–Next Generation EU (2021/PER/00020). PJC-Y was supported by a Post-Doctoral Fellowship from Generalitat Valenciana (APOSTD/2019/009). TZ and AZ were supported by grant RSF 22-14-00084 from the Russian Academy of Sciences. The contribution of the crew and technicians of the RV Vereshchagin of the Irkutsk Limnological Institute is gratefully acknowledged

Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat

Lake Baikal is the deepest lake in the world. Its depth provides the only bathypelagic (> 1000 m deep) freshwater habitat on Earth and its oxic, ultra-oligotrophic features make it a freshwater counterpart of the deep ocean. Here we have analyzed metagenomes from 1250 and 1350 m deep samples and built 231 metagenome-assembled genomes (MAGs). We detected high fractions of Thaumarchaeota (ca. 20% of 16S rRNA reads) and members of the candidate phyla radiation (CPR) (3–4.5%). Among the MAGs, we obtained ammonia-oxidizing archaea (AOA, Nitrosopumilaceae) and bacteria (AOB, Nitrosomonadaceae), and nitrite-oxidizers (Nitrospirae) indicating very active nitrification. A new clade of freshwater SAR202 Chloroflexi and methanotrophs (Methyloglobulus) were also remarkably abundant, the latter reflecting a possible role of methane oxidation as well. Novel species of streamlined and cosmopolitan bacteria such as Ca. Fonsibacter or acI Actinobacteria were more abundant at the surface but also present in deep waters. Conversely, CPRs, Myxococcales, Chloroflexi, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) archaea, or Gammaproteobacteria were found only in bathypelagic samples. We noted various important taxonomic and metabolic differences between deep aphotic region of Lake Baikal and marine waters of similar depth: Betaproteobacteriales, CPR, and DPANN superphylum were only found in bathypelagic Baikal, while Deltaproteobacteria, Gammaproteobacteria, or Alphaproteobacteria prevailed in oceanic samples. The genes mediating ammonia and methane oxidation, aromatic compound degradation, or alkane/methanesulfonate monooxygenases were detected in higher numbers in deep Baikal compared to their oceanic counterparts or its own surface. Overall, depth seems to be less relevant than salinity in configuring the microbial community

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 Pelagibacter ubique strains, as well as a phage infecting the widespread freshwater bacterium Polynucleobacter

Jelly-like Microbial Mats over Subsurface Fields of Gas Hydrates at the St. Petersburg Methane Seep (Central Baikal)

<div><p>Jelly-like microbial mat samples were collected from benthic surfaces at the St. Petersburg methane seep located in Central Baikal. The concentrations of certain ions, specifically chloride, bromide, sulphate, acetate, iron, calcium, and magnesium, were 2–40 times higher in the microbial mats than those in the pore and bottom water. A large number of diatom valves, cyanobacteria, and filamentous, rod-shaped and coccal microorganisms were found in the samples of bacterial mats using light, epifluorescence and scanning microscopy.Comparative analysis of a 16S rRNA gene fragment demonstrated the presence of bacteria and archaea belonging to the following classes and phyla: Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Verrucomicrobia, Cytophaga-Flavobacteria-Bacteroidetes, Cyanobacteria, and Euryarchaeota. The chemical composition and phylogenetic structure of the microbial community showed that the life activity of the mat occurs due to methane and its derivatives involved. Values of δ¹³C for the microbial mats varied from −73.6‰ to −65.8‰ and for animals from −68.9‰ to −36.6‰. Functional genes of the sequential methane oxidation (<i>pmoA</i> and <i>mxaF</i>) and different species of methanotrophic bacteria inhabiting cold ecosystems were recorded in the total DNA. Like in other psychroactive communities, the destruction of organic substances forming formed as a result of methanotrophy, terminates at the stage of acetate formation in the microbial mats of Lake Baikal (1,400 m depth). Its further transformation is limited by hydrogen content and carried out in the subsurface layers of sediments.</p></div