Enhanced biological phosphorus removal (EBPR) technologies, which are widely applied in wastewater treatment, are based on the activity of polyphosphate-accumulating organisms (PAOs). However, the transition from conventional systems to EBPR remains poorly understood. In this study, phosphorus removal performance and the succession of an activated sludge microbial community were investigated in a sequencing batch reactor during transition from the anoxic/aerobic process to the anaerobic/aerobic EBPR configuration. Reactor performance data combined with molecular analyses revealed that community development proceeded through three distinct stages. During the first 15-20 days, a community with a pronounced PAO phenotype was formed, in which representatives of the genus Azonexus predominated (up to 23.8%). From 15-20 days to 2 months, a pseudo-steady state was achieved, with stable phosphorus removal (36-51%) and sustained dominance of Azonexus (up to 23-18%). Then a shift in community structure occurred, marked by a decline of Azonexus (<1%) and an increase in Accumulibacter (up to 8.3%) and other potential PAOs (Comamonadaceae and Thiotrichaceae); however, phosphorus removal efficiency decreased to 27-31%. These results highlight the importance of considering microbial succession at the EBPR start-up to develop operational strategies that ensure sustainable phosphorus removal.

Denitrifying polyphosphate-accumulating organisms (DPAOs) enable simultaneous N and P removal, however, reliable strategies for enriching stable DPAO communities and their metabolic interactions remain insufficiently understood. In this study, DPAO-enriched cultures were developed in a sequencing batch reactor operated under anaerobic/anoxic conditions with acetate as C source. For three independent experiments, activated sludge, collected at different times, was used as the inoculum. Within 0.5-2 months, all experiments exhibited definitive DPAO phenotype dynamics. After 100-200 days of operation, the microbial community was consistently co-dominated by two genera: Azonexus (19-35 %), representing DPAOs, and Competibacter (23-31 %), representing denitrifying glycogen-accumulating organisms (DGAOs). Metagenomic reconstruction revealed that neither Azonexus nor Competibacter harbored the full complement of denitrification genes. The Azonexus metagenome-assembled genome encoded napAB (nitrate reductase), nirS (nitrite reductase), and nosZ (nitrous oxide reductase), while the Competibacter MAG possessed only norBC (nitric oxide reductase) genes. This genomic complementarity provides evidence that complete denitrification in this system could be achieved through cooperation between DPAOs and DGAOs. Consequently, the observed lower phosphorus removal efficiency, compared to anaerobic/aerobic systems, is attributed to the reduced biomass yield of DPAOs and the high essential abundance of DGAOs. These results clarify the ecological role of Azonexus as a DPAO dependent on partnership with DGAOs. Furthermore, the selective conditions favoring Azonexus development in enhanced nutrient removal systems, are evaluated. This work reveals a possible mechanism of syntrophic cooperation between DPAO and DGAO, which has direct implications for the development of resource-saving biological processes for nutrient removal.

Schizosaccharomyces pombe is a non-Saccharomyces yeast that is widely used in winemaking due to its ability to ferment malic acid, thus improving organoleptic properties of wine. We report the draft genome sequence of S. pombe strain I-540, isolated from grape must in Russia.

The use of seawater with a high sulfate content for water-flooding of oil reservoirs contributes to the growth of sulfate-reducing bacteria (SRB), producing sulfide, which causes oil souring, corrosion of steel equipment, and environmental problems during oil production and refining. The purpose of this work was to determine the composition of microorganisms and the physicochemical parameters of the production and injection water of the Prirazlomnoye offshore high-temperature oil field in order to improve our understanding of the corrosion-active microorganisms. High-throughput sequencing of V3-V4 fragments of the 16S rRNA gene, quantitative PCR of bacteria and archaea, and cultural and analytical methods were used in the work. SRB, fermentative and syntrophic bacteria, and methanogenic archaea capable of participating in the processes of general and pitting corrosion of steel equipment were found in water samples. The production water contains sulfate, sulfide, and thermophilic SRB (Thermacetogenium and Desulfonauticus). Mixing of the produced water with seawater leads to its cooling and emergence of mesophilic SRB (Desulfobacter and Desulfogranum) in the water treatment system. Residual oil hydrocarbons and sulfides can be oxidized in the water treatment system, and the resulting metabolites serve as electron donors and acceptors for fermentative sulfidogenic bacteria (genera Caminicella, Kosmotoga, Petrotoga, and Geotoga). Sulfate-reducing and methanogenic enrichments from reservoir water produce sulfide and methane, respectively, receiving electrons from Fe0 in the absence of other sources of H2, which can contribute to pitting corrosion. This study allows for improving the ways to control sulfidogens and expands understanding of the microbial diversity of oil reservoirs.IMPORTANCEOil production from oil reservoirs with sulfate-containing formation water and injection seawater is accompanied by the appearance of sulfide in oil production, which increases the cost of oil refining and enhances corrosion processes of steel equipment. In this work, the physicochemical conditions and the composition of microorganisms in the produced and injected seawater at the Prirazlomnoye oil field (Russia) are investigated. The biocides used at the oil field are ineffective in suppressing sulfate-reducing bacteria (SRB), which are considered the main agents of microbial corrosion. It has been shown that not only SRBs but also fermenting bacteria inhabiting the oilfield were capable of producing sulfide. Enrichment cultures of autotrophic SRBs and methanogens capable of receiving electrons directly from Fe0 with the production of sulfide and methane, respectively, were obtained. The new scientific information obtained on microbial communities of oil reservoirs will make it possible to improve methods for monitoring corrosive microorganisms and selecting biocides.

Oil reservoirs with carbonate oil-bearing collectors are characterized by high fracturing. To improve the coverage of a reservoir by flooding, clogging agents should be introduced into the formation. In the patent literature, using sapropel as a plugging agent has been proposed. In the present work, application of cultural methods revealed that sapropel can be not only a dispersant, but also a source of aerobic hydrocarbon-oxidizing and anaerobic fermenting bacteria. Taxonomic analysis of the sapropel microbial community using high-throughput sequencing of the 16S rRNA gene V3–V4 region showed predominance of bacteria of the genus Streptomyces (40.7

The goal of the present work was to perform biooxidation of a gold-bearing pyrite-arsenopyrite flotation concentrate under unfavorable conditions (decreased retention time). For this purpose, biooxidation of the concentrate containing 51

Microbial communities in wastewater treatment plants (WWTPs) play a crucial role in the decontamination of polluted water. An uncultured order-level lineage AKYH767 of the phylum Bacteroidota has been consistently detected in microbial consortia of activated sludge at WWTPs worldwide, but its functional role remains elusive. Representatives of AKYH767 were also detected in soils and freshwater bodies, which may be their natural reservoirs. Here, we obtained ten high-quality metagenome-assembled genomes, including one closed circular genome, of AKYH767 bacteria from metagenomes of the wastewater and activated sludge and used genomic data to uncover the metabolic potential of these bacteria and to predict their functional role. The cells of the AKYH767 bacteria were inferred to be rod-shaped and non-motile. Genome-based metabolic reconstruction predicted the Embden–Meyerhof pathway, the non-oxidative stage of the pentose phosphate pathway, and the complete tricarboxylic acid cycle. A facultatively anaerobic chemoheterotrophic lifestyle with the capacity to oxidize low organic substrates through aerobic respiration was suggested. Under anaerobic conditions AKYH767 bacteria can perform different steps of denitrification. They have limited capacities to hydrolyze carbohydrates and proteinaceous substrates but can utilize fatty acids. A peculiar property of AKYH767 bacteria is the presence of the phenylacetyl-CoA pathway for the utilization of phenylacetate, and about half of the genomes encoded the benzoate degradation pathway. Apparently, in bioreactors at WWTPs, the AKYH767 bacteria could be involved in the denitrification and biodegradation of aromatic compounds. Based on phylogenetic and genomic analyses, the novel AKYH767 bacterium is proposed to be classified as Candidatus Pollutiaquabacter aromativorans, within the candidate order Pollutiaquabacterales.

Responses of the anammox bacterial community (oxidizing ammonium with nitrite and releasing gaseous nitrogen) to acidification and alkalization of the medium were different. While acidic shock caused temporary inhibition of bacterial activity, but not their death, alkaline shock resulted in death of most nitrifiers and anammox bacteria. Addition of chalk powder (CaCO3) as a pH-stabilizing agent was sufficient for prevention of acidic shock or overcoming its effects. Introduction of additional activated sludge proved efficient for rapid restoration of the anammox rate after alkaline shock. The sludge identical to that present in the reactor was more efficient than the sludge grown under other conditions.

Extremely acidophilic iron- and sulfur-oxidizing bacteria and archaea are used in the processing of different sulfide ores and concentrates (biohydrometallurgical technologies); therefore, studying their metabolic pathways and regulation is an urgent task. Thus, the goal of this work was to compare differential gene expression in the thermoacidophilic archaeal strain, representative of the genus Acidiplasma, a predominant microbial group in bioleach reactors, during growth in the presence of ferrous iron and elemental sulfur as well as pyrite and arsenopyrite, which are the most widespread sulfide minerals, and to obtain novel data on the mechanisms of interaction of microorganisms and sulfide minerals. Transcriptomic analysis revealed metabolic pathways involved in ferrous iron and sulfur oxidation (key processes in sulfide mineral oxidation) and determined their expression dependence on different substrates. It was shown that the blue copper protein sulfocyanin may play an important role in both iron and sulfur oxidation, while sulfur oxidation also involves genes encoding well-known proteins for reduced inorganic sulfur compounds (RISC), sulfur oxygenase reductase (SOR), and thiosulfate quinone oxidoreductase (TQO). The results obtained in the present study may be used in further work to improve biohydrometallurgical technologies.

Genome reduction and associated metabolic deficiencies have been described in various lineages of parasitic and symbiotic microorganisms that obtain essential nutrients from their partners, and in some free-living microorganisms that inhabit stable environments. The animal gut is a relatively stable ecosystem, characterized by an abundance of organic substances and a high concentration of microorganisms, which provides favorable conditions for the survival of microorganisms with reduced genomes. Metagenomic analysis of 49 samples of feces of farm animals (cows, sheep, yaks, and horses) revealed uncultured lineages of bacteria with reduced genomes (<1 Mbp): family UBA1242 (Christensenellales, Firmicutes), order Rs-D84 (Alphaproteobacteria), and family UBA9783 (Opitutales, Verrucomicrobiota), defined in genome-taxonomy database. Analysis of the genomes showed that these bacteria lacked pathways for the biosynthesis of amino acids, nucleotides, lipids, and many other essential metabolites. The UBA9783 genomes encoded a near-complete Embden-Meyerhof glycolytic pathway and the non-oxidative phase of the pentose phosphate pathway, while in UBA1242 and Rs-D84, these pathways are incomplete. All bacteria are limited to fermentative metabolism and lack aerobic and anaerobic respiratory pathways. All UBA9783 and some Rs-D84 genomes encoded F0F1-type ATP synthase and pyrophosphate-energized proton pump; they also can import and utilize peptides and some amino acids. While UBA9783 bacteria could thrive as specialized free-living organisms in the organic-rich gut environment, the UBA1242 and Rs-D84 lineages appear to have adopted the lifestyle of an obligate symbiont/parasite, obtaining metabolites from other cells.IMPORTANCEThe microbiota of the animal gastrointestinal tracts is a complex community of microorganisms which interact in a synergistic or antagonistic relationship and play key nutritional and metabolic roles. However, despite its importance, the gut microbiota of farm animals, especially its uncultured majority, remains largely unexplored. We performed a metagenomic analysis of the gut microbiome of farm animals and characterized three uncultured lineages of bacteria with reduced genomes (<1 Mbp) from the phyla Firmicutes, Proteobacteria, and Verrucomicrobiota. These bacteria were predicted to possess key metabolic deficiencies such as the inability to synthesize essential cell metabolites, suggesting their adaptation to the lifestyle of a symbiont/parasite, or a scavenger obtaining nutrients from the organic-rich gut environment. This study shows that genome reduction with metabolic specialization and adaptation to a partner-dependent lifestyle occurred through convergent evolution in several phylogenetically distant lineages of gut microbiota.

In a sequentially periodic bioreactor, changes in the structure and properties of a community enriched with phosphate-accumulating microorganisms (PAO) after a shift in pH to more acidic values (pH 6.7–7.1) were traced. The proportion of Candidatus Accumulibacter decreased from 43.6 to 13.9%, while the number of potential FAOs belonging to Dechloromonas and Thauera increased. At the same time, the share of the total amount of FAO changed slightly and amounted to 40–43%. The share of the main competitors of FAO ‒ glycogen-accumulating microorganisms (GAM) during the experiment remained insignificant: Competibacter 16S rRNA gene fragments before and after pH changes amounted to 2‒4%. A decrease in pH led to a drop in the amount of phosphates released in the anaerobic phase, but the amount of phosphorus in the biomass and its removal remained high ‒ 15–17 and 92–94%, respectively.

Planctomycetes of the genus Singulisphaera are common inhabitants of soils and peatlands. Although described members of this genus are characterized as possessing hydrolytic capabilities, the ability to degrade chitin has not yet been reported for these bacteria. In this study, a novel Singulisphaera representative, strain Ch08, was isolated from a chitinolytic enrichment culture obtained from a boreal fen in Northern European Russia. The 16S rRNA gene sequence of this isolate displayed 98.2% similarity to that of Singulisphaera acidiphila MOB10T. Substrate utilization tests confirmed that strain Ch08 is capable of growth on amorphous chitin. The complete genome of strain Ch08 determined in this study was 10.85 Mb in size and encoded two predicted chitinases, which were only distantly related to each other and affiliated with the glycoside hydrolase family GH18. One of these chitinases had a close homologue in the genome of S. acidiphila MOB10T. The experimental verification of S. acidiphila MOB10T growth on amorphous chitin was also positive. Transcriptome analysis performed with glucose- and chitin-growth cells of strain Ch08 showed upregulation of the predicted chitinase shared by strain Ch08 and S. acidiphila MOB10T. The gene encoding this protein was expressed in Escherichia coli, and the endochitinase activity of the recombinant enzyme was confirmed. The ability to utilize chitin, a major constituent of fungal cell walls and arthropod exoskeletons, appears to be one of the previously unrecognized ecological functions of Singulisphaera-like planctomycetes.

A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (–)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (–)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.

For ammonium removal from wastewater, anammox technologies are among the most efficient and rapidly developing ones. Due to the low growth rate of anammox bacteria and their sensitivity to various inhibitors, technologies using attached biocenosis carriers (ABCs) provide for reliable operation. The goal of the present work was to investigate a new ABC type, ETEK biochips based on a nonwoven fibrous material. The work involved the techniques of materials science (design of a new ABC type) and physical modeling of the anammox process (in a laboratory bioreactor), as well as electron microscopy and molecular profiling of activated sludge communities. Comparison of the ETEK biochips with the ABCs of foamed polyethylene BF33 and Mutag revealed more rapid accumulation (5-fold) of the activated sludge biomass on ETEK biochips upon reactor launching, as well as comparable buoyancy and reactor productivity regarding N removal. The specific rate of nitrogen removal obtained with ETEK biochips considerably exceeded that for foamed polyethylene with a filler: 1.5–3 times higher per chip and 1.5 times higher per activated sludge biomass unit. The studied ABC shared the same issue of floating to the surface due to the active formation of gas (N2). The algorithm for calculating the downward flows in bioreactors with rapidly surfacing ABC is proposed, and a new hydrodynamic type of a bioreactor (with hybrid hydrodynamics) is described, a moving bed–sequencing batch reactor (MB-SBR).

Gold recovery from refractory pyrite-arsenopyrite concentrates using stirred tank reactor biooxidation is widely applied worldwide. Therefore, studies to address the characteristic problem of this technology are urgent. The goal of the present work was to research the possibility of counteracting the negative effects of unfavorable conditions (increasing pulp density and temperature) on the biooxidation of pyrite-arsenopyrite concentrate in laboratory-scale stirred tank reactors using additional carbon supply in the form of CO2. A refractory concentrate containing pyrite (48%) and arsenopyrite (13%) was used in biooxidation experiments. In the control experiment, biooxidation was performed under “normal conditions”: temperature 40 °C, pulp density (solid to liquid ratio, S:L) 1:10, residence time 5 days. It was shown that under “normal conditions”, additional carbon dioxide supply insignificantly affected the biooxidation rate and composition of the microbial population of biooxidation reactors. In addition, the effect of “stressful conditions” was studied. In this case, either temperature or pulp density were increased (up to 50 °C and S:L 1:5, respectively), which provided unfavorable conditions for biooxidation and led to the decrease in biooxidation rate. Under “stressful conditions”, additional carbon dioxide supply affected biooxidation to a greater extent and made it possible to increase both pyrite and arsenopyrite biooxidation rates. The analysis of microbial populations showed that additional carbon dioxide supply also changed their composition.

Wastewater treatment plants (WWTPs) are considered to be hotspots for the spread of antibiotic resistance genes (ARGs). We performed a metagenomic analysis of the raw wastewater, activated sludge and treated wastewater from two large WWTPs responsible for the treatment of urban wastewater in Moscow, Russia. In untreated wastewater, several hundred ARGs that could confer resistance to most commonly used classes of antibiotics were found. WWTPs employed a nitrification/denitrification or an anaerobic/anoxic/oxic process and enabled efficient removal of organic matter, nitrogen and phosphorus, as well as fecal microbiota. The resistome constituted about 0.05% of the whole metagenome, and after water treatment its share decreased by 3–4 times. The resistomes were dominated by ARGs encoding resistance to beta-lactams, macrolides, aminoglycosides, tetracyclines, quaternary ammonium compounds, and sulfonamides. ARGs for macrolides and tetracyclines were removed more efficiently than beta-lactamases, especially ampC , the most abundant ARG in the treated effluent. The removal efficiency of particular ARGs was impacted by the treatment technology. Metagenome-assembled genomes of multidrug-resistant strains were assembled both for the influent and the treated effluent. Ccomparison of resistomes from WWTPs in Moscow and around the world suggested that the abundance and content of ARGs depend on social, economic, medical, and environmental factors.

The goal of this work was to study the process of bioleaching of arsenic-containing polymetallic concentrate containing 16.0

Microbial diversity in the fecal samples of Bactrian camels in Transbaikalia under various grazing management (free grazing (group I), mixed (group II), and stall housing (group III)) was revealed using high-throughput sequencing of the 16S rRNA gene variable regions. The microbial community of the fecal microbiota was found to be diverse and to depend on the camel grazing management. The most common phyla of the camel fecal microbiota were Bacillota and Bacteroidota. The phylum Verrucomicrobiota was a codominant in the fecal microbiota of groups I and II of animals, and Actinomycetota, in the feces of camels of group III. Changes in the fecal microbiota structure and taxonomic diversity occurred as camel grazing management and feeding conditions changed. Free grazing resulted in high diversity of the prokaryotic community in the fecal microbiota. In addition, differences in taxonomic composition depending on sex were found, which were in the abundance of taxa rather than in their presence or absence. The results contribute to the current understanding of the fecal microbiota of camels under different management conditions and provide evidence of the influence of nutrition on the fecal microbiota under different management conditions. Our results may be useful for addressing the issues of reproduction and conservation of the Transbaikal camel (Camelus bactrianus).

The search for the microorganisms responsible for sulfide formation and corrosion of steel equipment in the oil fields of Tatarstan (Russia) resulted in the isolation of a new halotolerant strictly anaerobic sulfate-reducing bacterium, strain 5S69T. The cells were motile curved Gram-negative rods. Optimal growth was observed in the presence of 2.0–4.0% (w/v) NaCl, at pH 6.5, and at 23–28 °C under sulfate-reducing conditions. The isolate was capable of chemoorganotrophic growth with sulfate and other sulfoxides as electron acceptors, resulting in sulfide formation; and of pyruvate fermentation resulting in formation of H2 and acetate. The strain utilized lactate, pyruvate, ethanol, methanol, fumarate, and fructose, as well as H2/CO2/acetate for sulfate reduction. The genome size of the type strain 5S69T was 4.16 Mb with a G + C content of 63.0 mol%. On the basis of unique physiological properties and results of the 16S rRNA gene-based phylogenetic analysis, phylogenomic analysis of the 120 conserved single copy proteins and genomic indexes (ANI, AAI, and dDDH), assigning the type strain 5S69T ((VKM B-3653T = KCTC 25499T) to a new species within the genus Pseudodesulfovibrio, is suggested, with the proposed name Pseudodesulfovibrio methanolicus sp. nov. Genome analysis of the new isolate showed several genes involved in sulfate reduction and its sulfide-producing potential in oil fields with high saline formation water.