Root microbiomes of Zygophyllaceae in the Kazakhstan desert: a weak evidence for rhizobial nitrogen fixation , Vladimir G. Onipchenko, Alexandra A. Klyukina, , Ilya V. Kublanov, , Elizaveta A. Bonch-Osmolovskaya, , Dorzhi V. Badmadashiev, , M.T. Musabekov, , A.S. Bisengazieva, , Alexei V. Tiunov, , Sergey M. Tsurikov, , Asem A. Akhmetzhanova, , Tatiana G. Elumeeva, and Botanica Pacifica, 2024 The plants of the Zygophyllaceae family are often considered to be capable of symbiotic atmosphere nitrogen fixation, forming rhizobial nodules similar to those of Fabaceae and Urticaceae. In four species of Zygophyllaceae and the related Peganum harmala (hereafter called Z-plants), collected in Dzungarian deserts (Kazakhstan), we analyzed the prokaryotic component of the root microbiome and the 15N and 13C content in the leaves of these Z-plants compared with neighboring dicots belonging to other families (R-plants). Among all studied Zygophyllum fabago root samples only one was found to have the root nodule, however the microbiome of this sample was similar to that found in other Z. fabago root samples where nodulation was not observed. If compared to Z-plants, the R-plants had a significantly higher relative abundance of bacteria of genera Glycomyces, Massilia and Streptomyces, while the Z-plants had a higher relative abundance of the representatives of genera Actinomadura, Nocardia and Pseudonocardia. Unidentified representatives of the family Rhizobiaceae were present in some of R and Z plants, being most abundant in soil samples. On average, the Z- and the R-plants did not differ in their δ13С and δ15N. Overall, the results do not allow us to consider the studied Zygophyllaceae plants as species with effective atmospheric nitrogen fixation due to rhizobial symbiosis – a characteristic feature of the most legumes.
Stratification of Prokaryotic Communities in the White Sea Bottom Sediments D. V. Badmadashiev, A. R. Stroeva, A. A. Klyukina, E. N. Poludetkina, E. A. Bonch-Osmolovskaya Microbiology Russian Federation, 2023 Abstract— Investigation of prokaryotic communities from different horizons of the bottom sediments in the Kandalaksha Gulf, White Sea revealed two characteristic groups of sampling points. The first group demonstrated stratification of prokaryotic communities depending on the horizon depth, while the second one, with uniform prokaryotic communities, was typical of the sections with active organic matter decomposition. Microorganisms involved in decomposition of labile organic compounds (Woeseia and Sandaracinaceae), as well as sulfate reducers (SEEP-SRB1 and Sva0081) predominated in the upper horizons of the stratified sediments (the first group of samples). In the lower layers (30 and 50 cm), the share of microorganisms potentially involved in the degradation of complex compounds (e.g., Desulfatiglans, Hyphomicrobiaceae, and Mycobacterium) increased. The share of prokaryotes with unknown metabolism, such as JS1, SG8-4, WCHB1-81, Aerophobales, and S085, increased as well. Thus, the structure of prokaryotic communities was affected by the presence and abundance of organic matter, which decreased with depth.
Phylogenetic Diversity of Prokaryotic Communities of the Upper Sediment Layers of the Kandalaksha Bay, White Sea D. V. Badmadashiev, A. R. Stroeva, A. A. Klyukina, E. N. Poludetkina, E. A. Bonch-Osmolovskaya Microbiology Russian Federation, 2023 Abstract— Microbial communities of the sediments of the Kandalaksha Bay (White Sea) remain insufficiently studied. While the data on the rates of some microbial processes are available, very little is known about microorganisms inhabiting these sediments. In the this study, high-throughput sequencing of variable regions of 16S rRNA genes was used to characterize the microbial communities of 47 Kandalaksha Bay sediment samples collected at 10 cm below the bottom surface. Pseudomonadota and Desulfobacterota were the most abundant phyla, comprising together about a half of all prokaryotes. Determination of the dominant genus-level taxon proved impossible. The most represented chemoorganotrophic microorganisms were uncultured Sandaracinaceae (up to 10.8%) and Woeseia (up to 7.5%). Sulfate-reducing bacteria were important community components in the studied upper sediment layers, with uncultured groups SEEP-SRB1 (up to 7.0%) and Sva0081 (up to 5.9%) being the most abundant. In some samples, the genera Sulfurovum (up to 15.5%) and Thiohalophilus (up to 7.0%) involved in the oxidation of sulfur compounds were found to be important components of the community. Among the archaeal ASVs, the genus Nitrosopumilus oxidizing ammonium to nitrite exhibited the highest relative abundance (up to 6.9% of the total number of prokaryotes). Numerous sequences identified as the 16S rRNA gene fragments of chloroplasts were found in the samples, indicating that the rate of organic matter delivery to the upper sediment layers exceeded the rate of its degradation.
Molecular Biological Characteristics of Soil Microbiome in the Northern Part of the Novaya Zemlya Archipelago D. A. Nikitin, L. V. Lysak, D. V. Badmadashiev Eurasian Soil Science, 2022 Microbiomes of strongly skeletal residual calcareous pelozems (Skeletal Leptosols (Loamic)), carbopetrozems (Calcaric Leptosols (Protic)), petrozems (Skeletal Leptosols (Protic)), and cryozems (Oxyaquic Cryosols (Loamic)) in the north of Novaya Zemlya were studied by the methods of molecular biology. The number of copies of 16S rRNA genes was small and ranged from 2.30 × 107 to 1.63 × 109 gene copies/g soil for archaea and from 3.47 × 108 to 2.26 × 1011 gene copies/g soil for bacteria; the number of copies of ribosomal genes ITS rRNA of fungi varied from 8.87 × 106 to 7.56 × 109 gene copies/g soil. The content of copies of ribosomal genes of all groups of microorganisms sharply decreased down the soil profiles. Bacteria predominated among prokaryotes (up to 90%). The greatest abundance (20%) was manifested by the phyla Proteobacteria, Actinobacteria, and Acidobacteria; the abundances of Bacteroidetes, Firmicutes, Verrucomicrobia, Gemmatimonadetes, and Chloroflexi were about 1–10%. The Archaea domain represented mainly by the Ferroplasma genus (phylum Euryarchaeota), accounted for ≤4% of prokaryotes. The taxonomic diversity of prokaryotes increased down the soil profiles and reached maximum values in the suprapermafrost horizons, where the number of candidate phyla typical of marine ecosystems—Latescibacteria, Tectomicrobia, Parcubacteria, Saccaribacteria, Hydrogenedentes, Peregrinibacteria, Ignavibacteria, and Gracilibacteria—was high.
Biological Activity of Soils in the North of the Novaya Zemlya Archipelago: Effect of the Largest Glacial Sheet in Russia D. A. Nikitin, L. V. Lysak, D. V. Badmadashiev, S. S. Kholod, N. S. Mergelov, A. V. Dolgikh, S. V. Goryachkin Eurasian Soil Science, 2021 The vegetation cover and the chemical and physical properties of strongly skeletal residual-calcareous pelozems (Skeletic Leptosols (Loamic)), carbopetrozems (Calcaric Leptosols (Protic)), petrozems (Skeletic Leptosols (Protic)), and cryozems (Oxyaquic Cryosols (Loamic)) in the northern part of the Novaya Zemlya archipelago are described. The reserves and structure of microbial biomass, the intensity of СО2 (basal and substrate-induced respiration), СН4 (methanogenesis), and N2O (denitrification) emissions in the soil samples have been determined. The biomass of microorganisms (prokaryotes and fungi in total) varies from 22.50 to 390.18 μg/g soil. The share of mycobiota in the microbial biomass reaches 80–98%. Most of the microbial biomass (up to 50%) is concentrated in the surface horizons. The number of prokaryotes ranges from 1.5 × 107 to 9.66 × 108 cells/g soil, and the biomass of fungi varies from 22 to 372 μg/g soil. The length of the actinomycete mycelium is small: from 0.6 to 23.5 m/g soil, and the length of fungal hyphae is an order of magnitude higher (up to 166 m/g soil). All parameters of the biological activity of the studied soils sharply decrease down the soil profiles being positively correlated with the contents of organic matter, carbon, and nitrogen. In general, the values of the studied indicators of the biological activity of soils in the north of Novaya Zemlya are lower than those in soils located 3°–5° to the north, on Franz Josef Land. This phenomenon is explained by the influence of the largest glacier in Russia on the soil and vegetation cover on the adjacent territory in the north of Novaya Zemlya.
