The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton.

Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.

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.

Co-occurrence patterns between phytoplankton and bacterioplankton across the pelagic zone of Lake Baikal during spring.

Phytoplankton and bacterioplankton play a key role in carbon cycling of aquatic ecosystems. In this study, we found that co-occurrence patterns between different types of phytoplankton, bacterioplankton, and environmental parameters in Lake Baikal during spring were different over the course of three consecutive years. The composition of phytoplankton and bacterial communities was investigated using microscopy and 16S rRNA gene pyrosequencing, respectively. Non-metric multidimensional scaling (NMDS) revealed a relationship between the structure of phytoplankton and bacterial communities and temperature, location, and sampling year. Associations of bacteria with diatoms, green microalgae, chrysophyte, and cryptophyte were identified using microscopy. Cluster analysis revealed similar correlation patterns between phytoplankton abundance, number of attached bacteria, ratio of bacteria per phytoplankton cell and environmental parameters. Positive and negative correlations between different species of phytoplankton, heterotrophic bacteria and environmental parameters may indicate mutualistic or competitive relationships between microorganisms and their preferences to the environment.

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

The original version of this article unfortunately contained mistakes in the legends of figures.

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.

A family of silicon transporter structural genes in a pennate diatom Synedra ulna subsp. danica (Kütz.) Skabitsch.

Silicon transporters (SIT) are the proteins, which capture silicic acid in the aquatic environment and direct it across the plasmalemma to the cytoplasm of diatoms. Diatoms utilize silicic acid to build species-specific ornamented exoskeletons and make a significant contribution to the global silica cycle, estimated at 240 ±40 Tmol a year. Recently SaSIT genes of the freshwater araphid pennate diatom Synedra acus subsp. radians are found to be present in the genome as a cluster of two structural genes (SaSIT-TD and SaSIT-TRI) encoding several concatenated copies of a SIT protein each. These structural genes could potentially be transformed into "mature" SIT proteins by means of posttranslational proteolytic cleavage. In the present study, we discovered three similar structural SuSIT genes in the genome of a closely related freshwater diatom Synedra ulna subsp. danica. Structural gene SuSIT1 is identical to structural gene SuSIT2, and the two are connected by a non-coding nucleotide DNA sequence. All the putative "mature" SITs contain conserved amino acid motifs, which are believed to be important in silicon transport. The data obtained suggest that the predicted "mature" SIT proteins may be the minimal units necessary for the transport of silicon is S. ulna subsp. danica. The comparative analysis of all available multi-SITs has allowed us to detect two conservative motifs YQXDXVYL and DXDID, located between the "mature" proteins. Aspartic acid-rich DXDID motif can, in our opinion, serve as a proteolysis site during the multi-SIT cleavage. The narrow distribution of the distances between CMLD and DXDID motifs can serve as additional evidence to the conservation of their function.

Bacterial community composition in the water column of the deepest freshwater Lake Baikal as determined by next-generation sequencing.

The composition of bacterial communities in Lake Baikal in different hydrological periods and at different depths (down to 1515 m) has been analyzed using pyrosequencing of the 16S rRNA gene V3 variable region. Most of the resulting 34 562 reads of the Bacteria domain have clustered into 1693 operational taxonomic units (OTUs) classified with the phyla Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Firmicutes, Acidobacteria and Cyanobacteria. It has been found that their composition at the family level and relative contributions to bacterial communities distributed over the water column vary depending on hydrological period. The number of OTUs and the parameters of taxonomic richness (ACE, Chao1 indices) and diversity (Shannon and inverse Simpson index) reach the highest values in water layers. The composition of bacterial communities in these layers remains relatively constant, whereas that in surface layers differs between hydrological seasons. The dynamics of physicochemical conditions over the water column and their relative constancy in deep layers are decisive factors in shaping the pattern of bacterial communities in Lake Baikal.

Sub-Ice Microalgal and Bacterial Communities in Freshwater Lake Baikal, Russia.

The sub-ice environment of Lake Baikal represents a special ecotope where strongly increasing microbial biomass causes an "ice-bloom" contributing therefore to the ecosystem functioning and global element turnover under low temperature in the world's largest freshwater lake. In this work, we analyzed bacterial and microalgal communities and their succession in the sub-ice environment in March-April 2010-2012. It was found out that two dinoflagellate species (Gymnodinium baicalense var. minor and Peridinium baicalense Kisselew et Zwetkow) and four diatom species (Aulacoseira islandica, A. baicalensis, Synedra acus subsp. radians, and Synedra ulna) predominated in the microalgal communities. Interestingly, among all microalgae, the diatom A. islandica showed the highest number of physically attached bacterial cells (up to 67 ± 16 bacteria per alga). Bacterial communities analyzed with pyrosequencing of 16S rRNA gene fragments were diverse and represented by 161 genera. Phyla Proteobacteria, Verrucomicrobia, Actinobacteria, Acidobacteria, Bacteroidetes, and Cyanobacteria represented a core community independently on microalgal composition, although the relative abundance of these bacterial phyla strongly varied across sampling sites and time points; unique OTUs from other groups were rare.

The structure of microbial community and degradation of diatoms in the deep near-bottom layer of Lake Baikal.

Insight into the role of bacteria in degradation of diatoms is important for understanding the factors and components of silica turnover in aquatic ecosystems. Using microscopic methods, it has been shown that the degree of diatom preservation and the numbers of diatom-associated bacteria in the surface layer of bottom sediments decrease with depth; in the near-bottom water layer, the majority of bacteria are associated with diatom cells, being located either on the cell surface or within the cell. The structure of microbial community in the near-bottom water layer has been characterized by pyrosequencing of the 16S rRNA gene, which has revealed 149 208 unique sequences. According to the results of metagenomic analysis, the community is dominated by representatives of Proteobacteria (41.9%), Actinobacteria (16%); then follow Acidobacteria (6.9%), Cyanobacteria (5%), Bacteroidetes (4.7%), Firmicutes (2.8%), Nitrospira (1.6%), and Verrucomicrobia (1%); other phylotypes account for less than 1% each. For 18.7% of the sequences, taxonomic identification has been possible only to the Bacteria domain level. Many bacteria identified to the genus level have close relatives occurring in other aquatic ecosystems and soils. The metagenome of the bacterial community from the near-bottom water layer also contains 16S rRNA gene sequences found in previously isolated bacterial strains possessing hydrolytic enzyme activity. These data show that potential degraders of diatoms occur among the vast variety of microorganisms in the near-bottom water of Lake Baikal.