Elvira E. Ziganshina

Assessment of a biogas-generating microbial community in a pilot-scale anaerobic reactor

In this work bacteria and methanogenic archaea utilizing agricultural wastes in a pilot-scale biogas reactor were examined using sequencing and terminal restriction fragment length polymorphism analysis. Based on the analyses of 16S rRNA genes, Clostridia represented the most diverse group in the digester. Of the Clostridia, unclassified Clostridiales and the members of the genera Anaerotruncus and Tissierella were detected at high abundances. The representatives of the bacterial phyla Bacteroidetes and Proteobacteria were also defined, but in minor proportions, and were assigned to non-dominant communities. Within the phylum Euryarchaeota, the members of the orders Methanosarcinales and Methanomicrobiales were found at high levels. Methanogenic archaea were analyzed using both 16S rRNA and mcrA genes. Actually good results were received using both approaches; however, the rRNA gene method missed the non-dominant order Methanobacteriales.

Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters

Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake) was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors.

Comparison of anaerobic digestion strategies of nitrogen-rich substrates: Performance of anaerobic reactors and microbial community diversity

In the present study, the application of different operating strategies on performance of three continuous stirred tank reactors digesting chicken manure at mesophilic temperature and constant organic loading rate (OLR) of 3.5gVSL-1d-1 was investigated. Control reactor (RC) and reactor (RH) with the decreasing hydraulic retention time (HRT) had the comparable specific biogas production (SBP) with maximum values of 334-351mLg-1VS (added) during days 84-93, while the SBP from reactor with zeolites (RZ) was higher and achieved 426-432mLg-1VS (added). Attachments of microorganisms to zeolite particles as the operational environment, exchanged cations released from zeolites as well as lower total ammonium nitrogen (TAN) levels observed in RZ (6.2-6.3gL-1; days 71-93) compared to RC (6.6-6.9gL-1; days 71-93) resulted in a more effective process in RZ. Moreover, microbial community structure and dynamics were comprehensively characterized using Illumina sequencing, pyrosequencing and T-RFLP analysis of 16SrRNA genes. Methanogenic archaeal activity was additionally assessed by the expressed mcrA genes encoding the alpha subunit of methyl-CoM reductase. Within the major class Clostridia, Caldicoprobacter, Alkaliphilus, Gallicola, Sporanaerobacter and Tepidimicrobium spp. were the notable bacteria developed during operation of all tested reactors. Archaeal communities were dominated by methanogens belonging to the genus Methanosarcina followed by the genus Methanoculleus during the experimental period. Results of this study indicate that attachment of microorganisms to the zeolite particles as the operational environment might have led to the higher microbial activity at high ammonia concentrations.

Fe(III) mineral reduction followed by partial dissolution and reactive oxygen species generation during 2,4,6-trinitrotoluene transformation by the aerobic yeast Yarrowia lipolytica

Understanding the factors that influence pollutant transformation in the presence of ferric (oxyhydr)oxides is crucial to the efficient application of different remediation strategies. In this study we determined the effect of goethite, hematite, magnetite and ferrihydrite on the transformation of 2,4,6-trinitrotoluene (TNT) by Yarrowia lipolytica AN-L15. The presence of ferric (oxyhydr)oxides led to a small decrease in the rate of TNT removal. In all cases, a significant release of NO2− from TNT and further NO2− oxidation to NO3− was observed. A fraction of the released NO2− was abiotically decomposed to NO and NO2, and then NO was likely oxidized abiotically to NO2 by O2. ESR analysis revealed the generation of superoxide in the culture medium; its further protonation at low pH resulted in the formation of hydroperoxyl radical. Presumably, a fraction of NO released during TNT degradation reacted with superoxide and formed peroxynitrite, which was further rearranged to NO3− at the acidic pH values observed in this study. A transformation and reduction of ferric (oxyhydr)oxides followed by partial dissolution (in the range of 7–86% of the initial Fe(III)) were observed in the presence of cells and TNT. Mössbauer spectroscopy showed some minor changes for goethite, magnetite and ferrihydrite samples during their incubation with Y. lipolytica and TNT. This study shows that i) reactive oxygen and nitrogen species generated during TNT transformation by Y. lipolytica participate in the abiotic conversion of TNT and ii) the presence of iron(III) minerals leads to a minor decrease in TNT transformation.

Bacterial Communities Associated with Atherosclerotic Plaques from Russian Individuals with Atherosclerosis

Atherosclerosis is considered a chronic disease of the arterial wall and is the major cause of severe disease and death among individuals all over the world. Some recent studies have established the presence of bacteria in atherosclerotic plaque samples and suggested their possible contribution to the development of cardiovascular disease. The main objective of this preliminary pilot study was to better understand the bacterial diversity and abundance in human atherosclerotic plaques derived from common carotid arteries of individuals with atherosclerosis (Russian nationwide group) and contribute towards the further identification of a main group of atherosclerotic plaque bacteria by 454 pyrosequencing their 16S ribosomal RNA (16S rRNA) genes. The applied approach enabled the detection of bacterial DNA in all atherosclerotic plaques. We found that distinct members of the order Burkholderiales were present at high levels in all atherosclerotic plaques obtained from patients with atherosclerosis with the genus Curvibacter being predominant in all plaque samples. Moreover, unclassified Burkholderiales as well as members of the genera Propionibacterium and Ralstonia were typically the most significant taxa for all atherosclerotic plaques. Other genera such as Burkholderia, Corynebacterium and Sediminibacterium as well as unclassified Comamonadaceae, Oxalobacteraceae, Rhodospirillaceae, Bradyrhizobiaceae and Burkholderiaceae were always found but at low relative abundances of the total 16S rRNA gene population derived from all samples. Also, we found that some bacteria found in plaque samples correlated with some clinical parameters, including total cholesterol, alanine aminotransferase and fibrinogen levels. Finally, our study indicates that some bacterial agents at least partially may be involved in affecting the development of cardiovascular disease through different mechanisms.

Bacterial communities inhabiting toxic industrial wastewater generated during nitrocellulose production

Abstract Investigating the microbial community structure and composition of toxic industrial wastes contaminated with nitrocellulose and various by-products is crucial for understanding the fate of these pollutants in the environment and for the development and application of efiective bioremediation processes. In this study, we investigated the chemical properties and toxic potential of wastewater generated during nitrocellulose production. The analyzed wastewater from settling pond contained nitrocellulose powder particles as well as increased ammonium (570–760 mg/L), sulfate (1625– 2045 mg/L) and sulfite (864–1014 mg/L) concentrations. The toxicity test results demonstrated that the wastewater samples present acute toxicity for Paramecium caudatum and Daphnia magna. Furthermore, bacterial community structure in the samples was characterized by pyrosequencing of 16S rRNA genes. Phylogenetic analysis of bacterial sequences indicated that Proteobacteria, Bacteroidetes and Firmicutes were the main phyla in the sample near inlet, whereas various phylotypes of the phyla Proteobacteria, Chlorobi, Bacteroidetes and Gemmatimonadetes dominated in the sample near outlet. Some bacterial members observed in the current work can be considered as agents capable of performing biodegradation of various hazardous contaminants, indicating that the described bacterial communities have a high potential for the development of efiective bioremediation strategies.

Draft genome sequence of Brevibacterium epidermidis EZ-K02 isolated from nitrocellulose-contaminated wastewater environments

Brevibacterium spp. are aerobic, nonbranched, asporogenous, gram-positive, rod-shaped bacteria which may exhibit a rod-coccus cycle when cells get older and can be found in various environments. Several Brevibacterium species have industrial importance and are capable of biotransformation of various contaminants. Here we describe the draft genome sequence of Brevibacterium epidermidis EZ-K02 isolated from nitrocellulose-contaminated wastewater environments. The genome comprises 3,885,924 bp, with a G + C content of 64.2%. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession PDHL00000000.

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera)

Interpretation of how partnerships between fungi, bacteria, archaea, and insects are maintained through the life of the hosts is a big challenge within the framework of symbiosis research. The main goal of this work was to characterize the gut microbiota in larvae of several Coleoptera species using sequencing of the bacterial and archaeal 16S rRNA genes and fungal internal transcribed spacer (ITS) region. Thus, larvae with various food preferences, including Amphimallon solstitiale, Oryctes nasicornis, Cucujus cinnaberinus, Schizotus pectinicornis, Rhagium mordax, and Rhagium inquisitor, were thoroughly investigated in this work. We revealed an association of these beetle species mainly with four bacterial phyla, Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, as well as with three fungal phyla, Ascomycota, Zygomycota, and Basidiomycota, but microbial communities varied depending on the beetle host, individual organism, and surrounding environment. Moreover, archaea within the phyla Euryarchaeota and Crenarchaeota in the hindgut content of O. nasicornis and A. solstitiale were additionally detected. The identified microbial communities suggest their potential role in the exploitation of various resources, providing nutritional needs for the host organism. These microorganisms can also represent a valuable source of novel metabolic capacities for their application in different biotechnologies.