ALKALOHALOPHILIC BACTERIA OF THE FAMILY BACILLACEAE IN THE LAKES OF THE BADAIN JARAN DESERT (CHINA)

The Badain Jaran desert is located in the western part of Inner Mongolia (China) in the Alashan Highland. The investigated soda-salt lakes combine high pH (more than 9) and mineralization (up to 400 g/dm3), where conditions for the development of an alkali-halophilic microbial community are created. The purpose of our work was to isolate and study pure alkali-halophilic microorganisms in the lakes of the Badain Jaran desert. From the accumulative cultures of the cortex salt and the microbial mats of the lakes of the Badain Jaran desert, pure cultures belonging to the family Bacillaceae (the phylum Firmicutes) were isolated and described. With the help of biochemical methods, the ecological and physiological properties of the isolated bacteria were determined. The isolated bacteria exhibit the properties of alkalophiles and obligate alkalophiles and develop at pH 7–10.5, the optima ranging from 9 to 10. With respect to the concentration of NaCl, the strains showed the properties of obligate halophiles and extreme halophiles. With respect to temperature, the isolated microorganisms are mesophiles growing at 10–50 °C, the optimal growth being at 30–40 °C. With respect to the substrates used, the isolated cultures are noted for extensive metabolic activity and, when in their natural habitats, are supposedly active participants of the destruction of organic matter. To study the hydrochemical indicators of water, the following methods were used: atomic emission spectrometry with inductively coupled plasma, ion chromatography and capillary electrophoresis. As a result, it was found that a sodium cation and anions of carbonate, bicarbonate of chlorine and sulphate dominate in the soda-salt lakes of the Badain Jaran desert in a multicomponent composition. The results obtained broaden the notion of the diversity and ecological significance of bacteria in the extreme natural ecosystems of the Badain Jaran desert. The isolated strains are of interest for biotechnology as producers of enzymes resistant to high pH and mineralization

Description of a new species of soil algae, Parietochloris grandis sp. nov., and study of its fatty acid profiles under different culturing conditions

© 2018 Elsevier B.V. The new species Parietochloris grandis sp. nov. is described from forest soil in the Dnipropetrovsk region, Ukraine. The description is based on morphological features and the phylogenetic analysis of partial SSU rDNA and rbcL genes. Phylogenetic analysis places P. grandis in the Parietochloris clade, within the family Trebouxiophyceae. The novel strain formed a strongly supported monophyletic lineage with the type species of Parietochloris, P. alveolaris. P. grandis differed from other species in the Parietochloris clade by the size and form of vegetative cells and the large number of zoospores in zoosporangia. A number of experiments with different phosphates and nitrates concentrations were conducted to evaluate changes in fatty acid profile and biomass. The dominant fatty acids during cultivation on standard BG-11 medium, as well as with the phosphates concentrations ranged from 0.22 to 2 mM, were linoleic acid (24–25%), palmitic acid (12–14%), linolenic acid (9–12%), and oleic acid (7–11%). The content of arachidonic acid and eicosapentaenoic acid ranged from 3.5 to 4.5% and 0.7% to 0.8%, respectively. The fatty acid profile and total fatty acids varied significantly under different nutrient deficiency. The greatest variation was found for oleic acid (9–46%) and linolenic acid (2–13%). The percentage of arachidonic acid was the highest with a standard nitrates concentration in the medium (5%) and the lowest in the absence of phosphates and nitrates (1.3–1.5%), but the absolute content in dry biomass was similar in all variants of the experiment (6.5–9.3 mg g−1 dry weight). The absence of nitrogen and both nitrogen and phosphorus led to a 3–fold increase in TFA in comparison with the control. Thus, this strain can be considered in biotechnological application as a potential producer of the essential linoleic acid or oleic acid

Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts

IntroductionIt has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis.MethodsIn this study, shotgun metagenomic sequencing was used to investigate the microbiome in pox lesions from hosts infected with lumpy skin disease virus and sheep pox virus.ResultsThe analysis revealed a high degree of variability in bacterial community structures across affected skin samples, indicating the importance of specific commensal microorganisms colonizing individual hosts. The most common and abundant bacteria found in scab samples were Fusobacterium necrophorum, Streptococcus dysgalactiae, Helcococcus ovis and Trueperella pyogenes, irrespective of host. Bacterial reads belonging to the genera Moraxella, Mannheimia, Corynebacterium, Staphylococcus and Micrococcus were identified.DiscussionThis study is the first to investigate capripox virus-associated changes in the skin microbiome using whole-genome metagenomic profiling. The findings will provide a basis for further investigation into capripoxvirus pathogenesis. In addition, this study highlights the challenge of selecting an optimal bioinformatics approach for the analysis of metagenomic data in clinical and veterinary practice. For example, direct classification of reads using a kmer-based algorithm resulted in a significant number of systematic false positives, which may be attributed to the peculiarities of the algorithm and database selection. On the contrary, the process of de novo assembly requires a large number of target reads from the symbiotic microbial community. In this work, the obtained sequencing data were processed by three different approaches, including direct classification of reads based on k-mers, mapping of reads to a marker gene database, and de novo assembly and binning of metagenomic contigs. The advantages and disadvantages of these techniques and their practicality in veterinary settings are discussed in relation to the results obtained

Microbial diversity and biogeochemical cycling in soda lakes

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art ‘meta-omic’ techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments

Description of a new species of soil algae, Parietochloris grandis sp. nov., and study of its fatty acid profiles under different culturing conditions

© 2018 Elsevier B.V. The new species Parietochloris grandis sp. nov. is described from forest soil in the Dnipropetrovsk region, Ukraine. The description is based on morphological features and the phylogenetic analysis of partial SSU rDNA and rbcL genes. Phylogenetic analysis places P. grandis in the Parietochloris clade, within the family Trebouxiophyceae. The novel strain formed a strongly supported monophyletic lineage with the type species of Parietochloris, P. alveolaris. P. grandis differed from other species in the Parietochloris clade by the size and form of vegetative cells and the large number of zoospores in zoosporangia. A number of experiments with different phosphates and nitrates concentrations were conducted to evaluate changes in fatty acid profile and biomass. The dominant fatty acids during cultivation on standard BG-11 medium, as well as with the phosphates concentrations ranged from 0.22 to 2 mM, were linoleic acid (24–25%), palmitic acid (12–14%), linolenic acid (9–12%), and oleic acid (7–11%). The content of arachidonic acid and eicosapentaenoic acid ranged from 3.5 to 4.5% and 0.7% to 0.8%, respectively. The fatty acid profile and total fatty acids varied significantly under different nutrient deficiency. The greatest variation was found for oleic acid (9–46%) and linolenic acid (2–13%). The percentage of arachidonic acid was the highest with a standard nitrates concentration in the medium (5%) and the lowest in the absence of phosphates and nitrates (1.3–1.5%), but the absolute content in dry biomass was similar in all variants of the experiment (6.5–9.3 mg g−1 dry weight). The absence of nitrogen and both nitrogen and phosphorus led to a 3–fold increase in TFA in comparison with the control. Thus, this strain can be considered in biotechnological application as a potential producer of the essential linoleic acid or oleic acid