Bioaugmentation of Anammox Activated Sludge with a Nitrifying Bacterial Community as a Way to Increase the Nitrogen Removal Efficiency

Abstract—

Bioaugmentation, i.e., increasing the abundance of certain microorganisms in the community by adding appropriate cells or establishing the conditions promoting their growth, is widely used in environmental technologies. Its application for launching of the anammox reactors is usually limited to introduction of anammox bacteria. We expected addition of nitrifiers during anammox bioreactor launching to stimulate the anammox process due to rapid production of nitrite, which anammox bacteria use for ammonium oxidation. The present work investigated the effect of introduction of a nitrifying community on the composition and activity of the microbial community in an anammox reactor. At the time of inoculation of a laboratory SBR reactor, an active nitrifying community (5 days old) (ASB) (bioaugmenting activated sludge, ASB) containing group I nitrifiers, primarily Nitrosospira, was added (1 : 100 by biomass) to anammox activated sludge (ASA) stored for 1 month at 4°C and exhibiting low metabolic activity. The use of ASB resulted in increased efficiency of nitrogen removal. While noticeable nitrogen removal in the control (7%) was observed since day 11 of incubation, nitrogen removal in the experimental reactor began on day 4 at the level of 20%. Nitrogen removal after 30 days of incubation was ~60% in the experiment and 20% in the control. The rate of ammonium oxidation in the presence of ASB increased due to activity of nitrifying bacteria (during the first 10 days of operation) and anammox bacteria of the genus Brоcadia, which were already present in ASA (throughout all period of operation). Activity of group II nitrifiers (genera Nitrobacter and Nitrococcus), which were present in ASB, prevented accumulation of nitrite, which in high concentrations is toxic to both nitrifiers and anammox bacteria. High activity of the Nitrosospira nitrifiers introduced with ASB probably provided the anammox bacteria with one of the substrates (nitrite), promoting their rapid growth. During subsequent operation of the reactor, nitrifiers of the genus Nitrosomonas from the initial ASA community were mainly responsible for growth of the anammox bacteria. Thus, ASA bioaugmentation at the loading of the anammox reactor by active nitrifiers resulted in significantly improved efficiency of ammonium removal via the anammox process and accelerated transition of the reactor to the working mode.

Metagenomic Analysis of the Microbial Community in the Underground Coal Fire Area (Kemerovo Region, Russia) Revealed Predominance of Thermophilic Members of the Phyla Deinococcus-Thermus, Aquificae, and Firmicutes

Abstract

Underground burning of coal seams accompanied by release of gases leads to development of local thermal ecosystems. We investigated the microbial community of the ground heated to 72°C in the release area of hot gases resulting from underground combustion of coal mining waste at the Bungurskiy-Severny coal deposit in the Kemerovo region of Russia. Analysis of the composition of the microbial community by 16S rRNA gene profiling revealed predominance of thermophilic bacteria of the phyla Deinococcus-Thermus, Aquificae, and Firmicutes. As a result of metagenomic analysis, 18 genomes of the main members of the microbial community were assembled, including the complete genomes of Hydrogenobacter thermophiles, a member of the candidate genus UBA11096 of the phylum Aquificae (RBS10-58), Thermoflexus hugenholtzii, and Thermus antranikianii. Analysis of the RBS10-58 genome indicates that this bacterium can autotrophically fix carbon in the reductive tricarboxylic acid cycle and obtain energy via oxidation of hydrogen and sulfur compounds with oxygen or nitrate as electron acceptors. Genome analysis of the two dominant Firmicutes species, Hydrogenibacillus schlegelii and an uncultured member of the class Thermaerobacteria, showed that these bacteria could grow aerobically by oxidizing hydrogen and carbon monoxide. Overall, the community was dominated by aerobic bacteria capable of growing autotrophically and obtaining energy via oxidation of the main components of coal gases, hydrogen and carbon monoxide. Thermus antranikianii, which makes up about a half of the microbial community, probably uses organic matter produced by autotrophic members of Firmicutes and Aquificae.

Production of a Cloned Offspring and CRISPR/Cas9 Genome Editing of Embryonic Fibroblasts in Cattle

Somatic Cell Nuclear Transfer (SCNT) technique was used to produce the first viable cloned cattle offspring in Russia. Whole-genome SNP genotyping confirmed that the cloned calf was identical to the fibroblast cell line that was used for SCNT. CRISPR/Cas9 approach was subsequently used to knock out genes for beta-lactoglobulin gene (PAEP) and the beta-lactoglobulin-like protein gene (LOC100848610) in the fibroblast cells. Gene editing (GE) efficiency was 4.4% for each of these genes. We successfully obtained single-cell-derived fibroblast colonies containing PAEP and LOC100848610 knockouts, which will be used to produce beta-lactoglobulin-deficient cattle.

Identification and Expression Analysis of Chitinase Genes in Pitchers of Nepenthes sp. during Development

Fifteen chitinases of classes I-V were identified in the transcriptomes of pitchers and adult leaves of the carnivorous plant Nepenthes sp. Ten of these chitinases were identified for the first time, including the chitinases of classes II and V. The expression levels of all found chitinase genes in leaves and at three stages of pitcher development were determined. The maximum level of transcriptional activity in an open pitcher was observed for the genes encoding chitinase NChi4 (class II) and its isoforms. The expression levels of these genes significantly increased as the pitcher developed. In addition, for the first time, transcription of the genes encoding chitinases of all five classes was detected in the leaves of this plant.

Integrator is a key component of human telomerase RNA biogenesis

Telomeres are special DNA-protein structures that are located at the ends of linear eukaryotic chromosomes. The telomere length determines the proliferation potential of cells. Telomerase is a key component of the telomere length maintenance system. While telomerase is inactive in the majority of somatic cells, its activity determines the clonogenic potential of stem cells as a resource for tissue and organism regeneration. Reactivation of telomerase occurs during the process of immortalization in the majority of cancer cells. Telomerase is a ribonucleoprotein that contains telomerase reverse transcriptase and telomerase RNA components. The RNA processing mechanism of telomerase involves exosome trimming or degradation of the primary precursor. Recent data provide evidence that the competition between the processing and decay of telomerase RNA may regulate the amount of RNA at the physiological level. We show that termination of human telomerase RNA transcription is dependent on its promoter, which engages with the multisubunit complex Integrator to interact with RNA polymerase II and terminate transcription of the human telomerase RNA gene followed by further processing.

CONSTRUCTION OF MOSAIC HBC PARTICLES PRESENTING CONSERVATIVE FRAGMENTS OF M2 PROTEIN AND HEMAGGLUTININ OF INFLUENZA A VIRUS

Virus-like HBc particles formed as a result of the self-assembly of the nuclear antigen of the hepatitis B virus can be used as a highly immunogenic carrier for the presentation of foreign epitopes when creating recombinant vaccines. We use this vehicle to create influenza vaccines based on the conservative antigens of the influenza virus, the extracellular domain of the transmembrane protein M2 (M2e) and the fragment of the second subunit of hemagglutinin (HA2). Presentation on the surface of HBc particles should improve the immunogenicity of these peptides. Using genetic engineering techniques, we obtained a fusion protein in which the HA2 sequence is attached to the N-terminus of the HBc antigen, and the M2e peptide is included in the immunodominant loop region exposed on the surface of HBc particle. The hybrid protein expressed in Escherichia coli and purified under denaturing conditions formed virus-like HBc particles after refolding in vitro. Refolding of this protein in the presence of a previously denatured HBc antigen carrying no inserts resulted in formation of mosaic virus-like particles. The developed method will allow construction of mosaic HBc particles carrying different target epitopes of the influenza virus by combining the corresponding modified HBc proteins, which opens the possibility of creating vaccines with a wider spectrum of protection.

IMMUNOGENIC PROPERTIES OF RECOMBINANT MOZAIC PROTEINS BASED ON ANTIGENS NS4A AND NS4B OF HEPATITIS C VIRUS

The aim of the study was to investigate immunogenic properties of mosaic recombinant proteins constructed on the data of hepatitis C virus NS4A and NS4B antigens. Four mosaic recombinant proteins, containing the T and B epitopes of the NS4A and NS4B antigens, were created by genetic engineering methods in the E. coli system. To enhance the immune response they were linked in different variations to the nucleotide sequences of murine interleukin-2 (IL-2), the Neisseria meningiditis lipopeptide, and the T helper epitope of the core protein of hepatitis C virus. The immunogenic properties of these recombinant proteins were analyzed by immunoblotting, ELISA and ELISpot using sera from immunized mice and patients infected with hepatitis C virus. Recombinant proteins specifically reacted with the sera of immunized mice and infected patients in immunoblotting. According to the ELISA data, the predominant formation of antibodies to NS4B was observed when mice were immunized with the recombinant proteins containing both antigens. Analysis of gamma-interferon production by T-lymphocytes upon contact with activated dendritic cells showed in ELISpot that the maximum production of this cytokine was detected when adjuvant components were located at the N- and C-ends of the recombinant protein. The highest level of gamma-interferon production during stimulation with this drug was detected in lymphocytes from the bone marrow and lymph nodes. The recombinant protein containing the T and B epitopes of NS4A and NS4B, murine IL-2 and the lipopeptide Neisseria meningiditis had the greatest immunostimulate effect among the four constructions. This recombinant protein formed nanoparticles of 100-120 nm in size.

Influence of the Linking Order of Fragments of HA2 and M2e of the influenza A Virus to Flagellin on the Properties of Recombinant Proteins

The ectodomain of the M2 protein (M2e) and the conserved fragment of the second subunit of hemagglutinin (HA2) are promising candidates for broadly protective vaccines. In this paper, we report on the design of chimeric constructs with differing orders of linkage of four tandem copies of M2e and the conserved fragment of HA2 (76-130) from phylogenetic group II influenza A viruses to the C-terminus of flagellin. The 3D-structure of two chimeric proteins showed that interior location of the M2e tandem copies (Flg-4M2e-HA2) provides partial -helix formation nontypical of native M2e on the virion surface. The C-terminal position of the M2e tandem copies (Flg-HA2-4M2e) largely retained its native M2e conformation. These conformational differences in the structure of the two chimeric proteins were shown to affect their immunogenic properties. Different antibody levels induced by the chimeric proteins were detected. The protein Flg-HA2-4M2e was more immunogenic as compared to Flg-4M2e-HA2, with the former offering full protection to mice against a lethal challenge. We obtained evidence suggesting that the order of linkage of target antigens in a fusion protein may influence the 3D conformation of the chimeric construct, which leads to changes in immunogenicity and protective potency.

Influence of the Linking Order of Fragments of HA2 and M2e of the influenza A Virus to Flagellin on the Properties of Recombinant Proteins

The ectodomain of the M2 protein (M2e) and the conserved fragment of the second subunit of hemagglutinin (HA2) are promising candidates for broadly protective vaccines. In this paper, we report on the design of chimeric constructs with differing orders of linkage of four tandem copies of M2e and the conserved fragment of HA2 (76-130) from phylogenetic group II influenza A viruses to the C-terminus of flagellin. The 3D-structure of two chimeric proteins showed that interior location of the M2e tandem copies (Flg-4M2e-HA2) provides partial α-helix formation nontypical of native M2e on the virion surface. The C-terminal position of the M2e tandem copies (Flg-HA2-4M2e) largely retained its native M2e conformation. These conformational differences in the structure of the two chimeric proteins were shown to affect their immunogenic properties. Different antibody levels induced by the chimeric proteins were detected. The protein Flg-HA2-4M2e was more immunogenic as compared to Flg-4M2e-HA2, with the former offering full protection to mice against a lethal challenge. We obtained evidence suggesting that the order of linkage of target antigens in a fusion protein may influence the 3D conformation of the chimeric construct, which leads to changes in immunogenicity and protective potency.

[Identification and expression analysis of receptor-like kinase gene ERECTA in mycoheterotrophic plant Monotropa hypopitys]

The precise spatial-temporal coordination of cell division and differentiation is necessary for the correct formation of tissues, organs, and the organism as a whole. This coordination has been implemented by the intercellular communication mediated by signaling molecules and receptors that selectively recognize them. Membrane receptor kinases of ERECTA family regulate inflorescence and flower structure, the formation of root epidermis and adaptation responses. The characterization of the ERECTA genes of flowering plant pinesap Monotropa hypopitys with unique development features can enrich the knowledge about the kinase ERECTA functions and conserved development processes with their participation. Transcriptomic and genomic search with the subsequent structural-phylogenetic analysis identified the mRNA of a gene of serine-threonine kinase receptor with leucine-rich repeats of MhyERL1, which is the only ortholog of the ERECTA family kinases of pinesap. A quantitative analysis of the MhyERL1 gene transcripts has revealed its expression in all analyzed pinesap tissues with maximum levels in the flowers. MhyERL1 is probably involved in defining the inflorescence and flower architecture, and the formation of the pinesap root epidermis. The cascades involving ERL1 are apparently conserved. The exception are pathways associated with the development of above-ground vegetative structures, and the immune response to fungal pathogens probably lost in the process of the pinesap adaptation to unfavorable environmental conditions.

Identification and characterization of the flower meristem identity gene MhyLFY in mycoheterotrophic plant Monotropa hypopitys

The gene encoding the transcription factor LEAFY was identified in the genome of the mycoheterotrophic plant, pinesap Monotropa hypopitys. In the transcriptomes of roots, bracts, and flowers of flowering pinesaps, the MhyLFY gene expression was absent. These data suggest the conservativeness of the LFY-dependent mechanism of flower meristem identity and flower formation in heterotrophic species with some differences associated to the specificity of development and the structure of such plants. The pinesap flowering under the control of the transcription factor MhyLFY may be initiated either in an embryonic inflorescence during spring dormancy release of adventitious root buds or in an inflorescence of a growing reproductive stem after photoperiodic induction.

Identification and expression analysis of chitinase genes in parasitic plant Monotropa hypopitys

Genes encoding six chitinases, five of which belong to classes I (MhCHI3 and MhCHI4), IV (MhCHI1), V (MhCHI5), and VII (MhCHI2), were identified in the transcriptome of the parasitic mixoheterotrophic plant Monotropa hypopitys. The transcription level of MhCHI5 and MhCHI1 was low; however, in the leaves (bracts) and roots it was higher than in flowers. MhCHI4 transcripts were detected primarily in the flowers and were almost absent in the roots, whereas the expression level of MhCHI3 was relatively high in all organs but maximum in the leaves (bracts).