Assessment of Bacterial Community Composition of Anaerobic Granular Sludge in Response to Short-Term Uranium Exposure

Diatom DNA metabarcoding to assess the effect of natural radioactivity in mineral springs on ASV of benthic diatom communities

Little is still known about the low dose effects of radiation on the microbial communities in the environment. Mineral springs are ecosystems than can be affected by natural radioactivity. These extreme environments are, therefore, observatories for studying the influence of chronic radioactivity on the natural biota. In these ecosystems we find diatoms, unicellular microalgae, playing an essential role in the food chain. The present study aimed to investigate, using DNA metabarcoding, the effect of natural radioactivity in two environmental compartments (i.e. spring sediments and water) on the genetic richness, diversity and structure of diatom communities in 16 mineral springs in the Massif Central, France. Diatom biofilms were collected during October 2019, and a 312 bp region of the chloroplast gene rbcL (coding for the Ribulose Bisphosphate Carboxylase) used as a barcode for taxonomic assignation. A total of 565 amplicon sequence variants (ASV) were found. The dominant ASV were associated with Navicula sanctamargaritae, Gedaniella sp., Planothidium frequentissimum, Navicula veneta, Diploneis vacillans, Amphora copulata, Pinnularia brebissonii, Halamphora coffeaeformis, Gomphonema saprophilum, and Nitzschia vitrea, but some of the ASVs could not be assigned at the species level. Pearson correlation failed to show a correlation between ASV' richness and radioactivity parameters. Non-parametric MANOVA analysis based on ASVs occurrence or abundances revealed that geographical location was the main factor influencing ASVs distribution. Interestingly, ²³⁸U was the second factor that explained diatom ASV structure. Among the ASVs in the mineral springs monitored, ASV associated with one of the genetic variants of Planothidium frequentissimum was well represented in the springs and with higher levels of ²³⁸U, suggesting its high tolerance to this particular radionuclide. This diatom species may therefore represent a bio-indicator of high natural levels of uranium.

Microbial characteristic and bacterial community assessment of sediment sludge upon uranium exposure

The microbial characteristics and bacterial communities of sediment sludge upon different concentrations of exposure to uranium were investigated by high solution transmission electron microscopy (HRTEM), energy dispersive X-ray spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS) and high-throughput sequencing. After exposure to initial uranium concentrations of 10-50 μM for 24 h in synthetic wastewater, the removal efficiencies of uranium reached 80.7%-96.5%. The spherical and short rod bacteria were dominant in the sludge exposed to uranium. HRTEM-EDS and XPS analyses indicated that reduction and adsorption were the main mechanisms for uranium removal. Short-term exposure to low concentrations of uranium resulted in a decrease in bacterial richness but an increase in diversity. A dramatic change in the composition and abundances of the bacterial community were present in the sediment sludge exposed to uranium. The highest removal efficiency was identified in the sediment sludge exposed to 30 μM uranium, and the dominant bacteria included Acinetobacter (44.9%), Klebsiella (20.0%), Proteiniclasticum (6.7%), Enterobacteriaceae (6.6%), Desulfovibrio (4.4%), Porphyromonadaceae (4.1%), Comamonas (2.4%) and Sedimentibacter (2.3%). By comparison to the inoculum sediment sludge, exposure to uranium caused a substantial difference in the majority of bacterial abundance.

Spatial variation of sediment bacterial community in an acid mine drainage contaminated area and surrounding river basin

Microbial community is sensitive to the variations of environment, and it plays an important role in biogeochemical cycling in acid mine drainage (AMD). In this study, an integrated high-throughput absolute abundance quantification (iHAAQ) method was applied to study the dynamics of microbial community and the characteristics of microorganism. The results showed a significant difference in bacterial community with diversity being higher in watershed area. The main influential factors for bacterial communities in watershed were physicochemical properties (e.g., pH and potassium), while in mining areas the main driving factors were metals/metalloids (e.g., As, Zn, and Pb). Notably, the major functions of microbial community were transporter and ABC transporter in mining area, while two-component system was more abundant in watershed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis (level 3). In particular, Phyllobacterium, Bacteroides, and Sulfurovum were demonstrated to be potentially useful bacterial species for bioremediation, which should be a good choice for future studies. These results could facilitate our understanding of microbial diversity in different sediments of mining areas and identify microbial communities for bioremediation projects.

Trichococcus shcherbakoviae sp. nov., isolated from a laboratory-scale anaerobic EGSB bioreactor operated at low temperature

A new species of the genus Trichococcus, strain Art1^T, was isolated from a psychrotolerant syntrophic propionate-oxidizing consortium, obtained before from a low-temperature EGSB reactor fed with a mixture of VFAs (acetate, propionate and butyrate). The 16S rRNA gene sequence of strain Art1^T was highly similar to those of other Trichococcus species (99.7-99.9 %) but digital DNA-DNA hybridization values were lower than those recommended for the delineation of a novel species, indicating that strain Art1^T is a novel species of the genus Trichococcus. Cells of strain Art1^T are non-motile cocci with a diameter of 0.5-2.0 µm and were observed singularly, in pairs, short chains and irregular conglomerates. Cells of Art1^T stained Gram-positive and produced extracellular polymeric substances . Growth was optimal at pH 6-7.5 and cells could grow in a temperature range of from -2 to 30 °C (optimum 25-30 °C). Strain Art1^T can degrade several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate and ethanol. The genomic DNA G+C content of strain Art1^T is 46.7 %. The major components of the cellular fatty acids are C16 : 1 ω9c, C16 : 0 and C18 : 1 ω9c. Based on genomic and physiological characteristics of strain Art1^T, a new species of the genus Trichococcus, Trichococcusshcherbakoviae, is proposed. The type strain of Trichococcusshcherbakoviae is Art1^T (=DSM 107162^T = VKM B-3260^T).