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

Mallomonas kicherica Bessudova & Firsova & Tomberg & Bayramova & Hilkhanova & Bedoshvili & Bashenkhaeva & Zakharova & Likhoshway 2023, sp. nov.

<i>Mallomonas kicherica sp. nov.</i> Bessudova (Figs. 2–4). <p> <b>Description:</b> Scales are 3.4–4.5 × 1.8–2.4 μm, oval with lateral incurvings. The dome is subcircular with labyrinth-like reticulation. Small ribs extending to the first transverse rib extend from the dome towards the shield. The shield is patterned with of 8–11 regularly spaced transverse ribs. The transverse ribs, except for the area between the first and second (closest to the dome), are connected in random order by short ribs-jumpers (Figs. 2–4). The anterior flanges with 8–11 closely spaced struts on each side (Figs. 2–4). The anterior submarginal ribs are well-developed. The V-rib on the scales is acutely angled, hooded. The posterior rim is wide and smooth. The posterior flange contains approximately 20–23 struts (Figs. 2–4). Bristles are 6.5–9.2 μm in length, slightly curved (Fig. 2). The tip of the bristle is bifurcated with unequal diverging branches. One branch is short and sharp, whereas the other is wide with an acute tip and flat dorsal side. Cysts were not observed.</p> <p> <b>Holotype</b> (here designated): Portion of a single gathering of cells on SEM stub No. 18422 deposited at the herbarium of the Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk (LIN). Material from the Angara-Kichera estuary, a tributary of the northern part of Lake Baikal, was collected in June 2022. Figures 2–4 illustrates the characteristic scales from the holotype.</p> <p> <b>Type locality:</b> Mouth of the Kichera River, a tributary of the northern part of Lake Baikal, Republic of Buryatia, Russia. Latitude/Longitude: 55°43′55′′N, 109°32′24′′E.</p> <p> <b>Etymology:</b> The new species name is derived from the type locality, the Kichera River.</p> <p> <b>Distribution:</b> Up-to-date, <i>M. kicherica</i> has been only observed in its type locality. At the time of collection, pH = 8.04, T = 16.9°C, and EC = 112 μS̛ сm−1 (see Table 1).</p>Published as part of <i>Bessudova, Anna, Firsova, Alena D., Tomberg, Irina V., Bayramova, Elvira, Hilkhanova, Diana, Bedoshvili, Yekaterina D., Bashenkhaeva, Maria, Zakharova, Lyubov I. Kopyrina Yulia R. & Likhoshway, Yelena V., 2023, Two new species of silica-scaled chrysophytes (Chrysophyceae, Synurales) Mallomonas kicherica and M. sibirica water bodies of Eastern Siberia, Russia, pp. 59-69 in Phytotaxa 620 (1)</i> on pages 62-63, DOI: 10.11646/phytotaxa.620.1.5, <a href="http://zenodo.org/record/10015521">http://zenodo.org/record/10015521</a&gt

Mallomonas sibirica Bessudova & Firsova & Tomberg & Bayramova & Hilkhanova & Bedoshvili & Bashenkhaeva & Zakharova & Likhoshway 2023, sp. nov.

<i>Mallomonas sibirica sp. nov.</i> Bessudova (Figs. 5–11) <p> <b>Description:</b> Scales are 4.1–5.5 × 2.0–2.9 μm, oval, with lateral incurvings. The dome is subcircular, its ornamentation appears to vary between samples: smooth surface or with struts or rounded depressions (up to 0.15 μm in diameter) or reticulum variants were noted. The shield is covered with a thick secondary siliceous layer, marked with 8–12 regularly spaced transverse ribs with rounded depressions between them. Rounded depressions (up to 0.15 μm in diameter) are evenly distributed between the transverse ribs (Fig. 5, 6, 9). There is a pore on the basal plate inside each depression. A group of 8–10 pores is located in the angle of the V-rib in the posterior part of the shield (Fig. 5). This area is lacking the secondary siliceous layer. Anterior flanges are well-developed, with 2–8 (14) struts on each side (Figs. 7, 8). The V-rib on the scales is acutely angled, slightly hooded, and continues on the anterior flanges. The posterior rim is wide and smooth, bears numerous internal struts (Fig. 5). The posterior flange contains approximately 14–20 struts and scattered rounded depressions between them, that are not evenly spaced (Fig. 5). Bristles are 3.3–8.7 μm in length, slightly curved (Fig. 11). The tip is bifurcated with unequal diverging branches. One branch is short and sharp, whereas the other is wide with an acute tip and flat dorsal side. Cysts were not observed.</p> <p> <b>Holotype</b> (here designated): Portion of a single gathering of cells on SEM stubs No. 18075 deposited at the herbarium of the Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk (LIN). Y.R. Zakharova, Y.D. Bedoshvili and L.I. Kopyrina collected material from Ulu Lake, in the Republic of Yakutia, Russia, on April 24, 2021. Figure 6 illustrates illustrates the characteristic scales from the holotype.</p> <p> <b>Type locality:</b> Ulu Lake, Republic of Yakutia, Russia. Latitude/Longitude: N63º20ʹ9ʺ E141º3ʹ54ʺ.</p> <p> <b>Etymology:</b> The new species is named after the region of its origin, Siberia.</p> <p> <b>Distribution:</b> Up-to-date, <i>M. sibirica</i> have been recorded in the type locality and in other water bodies of Eastern Siberia: мixing zone of Yenisei River and Kara Sea waters; Vorota and Labynkyr lakes, Lake Baikal. <i>M. sibirica</i> was found at wide ranges of environmental parameters: pH from 6.97 to 9.34, specific conductance from 5.17 to 6560 μS̛ сm−1, and temperature of 0.4–10.2°C, salinity from 0.4 to 3.8 ‰ (see Table 1).</p>Published as part of <i>Bessudova, Anna, Firsova, Alena D., Tomberg, Irina V., Bayramova, Elvira, Hilkhanova, Diana, Bedoshvili, Yekaterina D., Bashenkhaeva, Maria, Zakharova, Lyubov I. Kopyrina Yulia R. & Likhoshway, Yelena V., 2023, Two new species of silica-scaled chrysophytes (Chrysophyceae, Synurales) Mallomonas kicherica and M. sibirica water bodies of Eastern Siberia, Russia, pp. 59-69 in Phytotaxa 620 (1)</i> on pages 64-65, DOI: 10.11646/phytotaxa.620.1.5, <a href="http://zenodo.org/record/10015521">http://zenodo.org/record/10015521</a&gt

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

The bacteria from the GenBank database most closely related, according to 16S rRNA gene sequences identified from deep near-bottom layer of Lake Baikal.

<p>The bacteria from the GenBank database most closely related, according to 16S rRNA gene sequences identified from deep near-bottom layer of Lake Baikal.</p

Bacterial isolates associated with the laboratory culture of <i>S. acus.</i>

<p><i> A. johnsonii</i> BW65UT1570 (A, F), <i>M. adhaesivum</i> BW66UT1570 (B), <i>A. tumefaciens</i> BW62UT1570 (D). The degradated siliceous frustules of diatom <i>S. acus</i> in cocultures with <i>B. simplex</i> BW64UT1570 (C), <i>A. johnsonii</i> BW65UT1570 (E). Axenic culture <i>S. acus</i> (G). Epifluorescent microscopy, DAPI staining (A, B); scanning electron microscopy (D, E, F, G). Scale bar: A, B and G, 50 µm; C, 40 µm; D, 10 µm; E, F, 5 µm.</p

Sample coverage, species richness and species diversity indices.

<p>Sample coverage, species richness and species diversity indices.</p