Регулирование информационного взаимодействия государственных органов с гражданами и организациями Украины

The system of a uniform information support of authorities and local management units is the integral part of information society and "E-government" of Ukraine. Its main objective is to provide efficiency for collection of information, creation of information resources, access to the information of authorities and the citizens, rise of efficiency of accepted solutions, support of information interactions of authorities; rendering real services from the state authorities to its citizens. Creation of such a system calls for enforcement issues inside the state bodies of the defined functions, development projects to define the rules in using interaction with citizens, implementations of the methods of process concepts and analysis of economic and social information

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. Acknowledgements We would like to thank Dr Robert Griffith/CEH for providing DNA from soil samples and Dr Anthony Travis for his help with BioLinux. Sequencing was performed in NERC platform in Liverpool. CG-R was funded by a NERC fellowship NE/J019151/1. CQ was funded by a MRC fellowship (MR/M50161X/1) as part of the cloud infrastructure for microbial genomics consortium (MR/L015080/1).Peer reviewedPublisher PD

Archaeal ammonia oxidation in volcanic grassland soils of Iceland. Effects of elevated temperature and N availability on processes and organisms

Thaumarchaea are recognized today as the most abundant and ubiquitously dis­tributed archaeal organisms, especially in the oceans and soil. Their phylogenetic placement as a phylum, the capability of all cultivated Thaumarchaea to oxidize ammonia for energy conservation as well as many further aspects concerning their ecology, physiology and evolution are discoveries of the last decade only. Still, conceptual knowledge on the role of Thaumarchaea in soil ammonia oxida­tion is lacking and their ecological significance in soils is poorly understood. The work presented in this thesis is concerned with archaeal ammonia-oxidizing communities in volcanic grassland soil in Grændalur, Iceland. The study site was chosen as it is remote enough from continental Europe to experience very little atmospheric N deposi­tion and because it contains grassland soils with different in situ temperatures as a result of geothermal heating. Several lines of evidence were gathered that Thaumarchaea are most likely of primary importance for ammonia oxidation in Grændalur, while ammonia-oxidizing bacteria (AOB) are present in numbers below the detection limit of conventional PCR (chapter 2, 4 and 5). Supposedly, this finding resembles a high ecological importance of AOA in terrestrial environments with low ammonia availability (chapter 4). Thaumarchaea could be stimulated in growth and activ­ity by N deposition in the form of ammonium, but only in low and medium concentrations of ~ 45 - 150 μg NH4+ - N per ∙ g dry soil-1. AOB however, were only responsive to medium and higher applications of ammonium (chapter 4). Through microcosm incubations it was identified that gross nitrification (i.e. the two step process by which ammonia is converted to nitrate with nitrite as intermedi­ary product) is functionally coupled to gross N mineralization in soils of Grændalur (chapter 3). By exposing the soils to short-term temperature changes however, this coupling of gross nitrification and gross N mineralization was lost and nitrifiers performed less well. This finding led to the conclusion that the nitrifying communities in Grændalur’s soils are adapted to function best at the temperature they experience in situ (chapter 3). In a stable-isotope labeling experiment with soil from Grændalur evidence for autotrophic growth of Nitrosopumilus-like Thaumarchaea, likely coupled to am­monia oxidation, was collected (chapter 5). Additionally, the results strongly sug­gested a syntrophic association between the autotrophically growing Thaumar­chaea and nitrite-oxidizing bacteria (NOB) of the Nitrospira sublineages I and II. The work of chapter 5 furthermore showed that the autotrophically active nitrifiers in this soil (i.e. Thaumarchaea and Nitrospira-like NOB) are stimulated by application of inorganic N in form of ammonium, but suppressed by the pres­ence of active methane-oxidizing bacteria (MOB). Likely, this negative interac­tion is a result of competition for common resources like inorganic N and oxygen. Intriguingly, growth of the total Thaumarchaeal community did not seize under conditions of suppressed net nitrification and autotrophic growth. In addition, the Thaumarchaeal community structure did not change. The data collected in this thesis therefore sug­gests that at least some Thaumarchaea possess the metabolic plasticity to choose for an energetically more advantageous mode of growth than lithoautotrophy by growing mixotrophically, possibly in association with mineralizers (chapters 3 and 5)

Archaeal ammonia oxidation in volcanic grassland soils of Iceland. Effects of elevated temperature and N availability on processes and organisms

Thaumarchaea are recognized today as the most abundant and ubiquitously dis­tributed archaeal organisms, especially in the oceans and soil. Their phylogenetic placement as a phylum, the capability of all cultivated Thaumarchaea to oxidize ammonia for energy conservation as well as many further aspects concerning their ecology, physiology and evolution are discoveries of the last decade only. Still, conceptual knowledge on the role of Thaumarchaea in soil ammonia oxida­tion is lacking and their ecological significance in soils is poorly understood. The work presented in this thesis is concerned with archaeal ammonia-oxidizing communities in volcanic grassland soil in Grændalur, Iceland. The study site was chosen as it is remote enough from continental Europe to experience very little atmospheric N deposi­tion and because it contains grassland soils with different in situ temperatures as a result of geothermal heating. Several lines of evidence were gathered that Thaumarchaea are most likely of primary importance for ammonia oxidation in Grændalur, while ammonia-oxidizing bacteria (AOB) are present in numbers below the detection limit of conventional PCR (chapter 2, 4 and 5). Supposedly, this finding resembles a high ecological importance of AOA in terrestrial environments with low ammonia availability (chapter 4). Thaumarchaea could be stimulated in growth and activ­ity by N deposition in the form of ammonium, but only in low and medium concentrations of ~ 45 - 150 μg NH4+ - N per ∙ g dry soil-1. AOB however, were only responsive to medium and higher applications of ammonium (chapter 4). Through microcosm incubations it was identified that gross nitrification (i.e. the two step process by which ammonia is converted to nitrate with nitrite as intermedi­ary product) is functionally coupled to gross N mineralization in soils of Grændalur (chapter 3). By exposing the soils to short-term temperature changes however, this coupling of gross nitrification and gross N mineralization was lost and nitrifiers performed less well. This finding led to the conclusion that the nitrifying communities in Grændalur’s soils are adapted to function best at the temperature they experience in situ (chapter 3). In a stable-isotope labeling experiment with soil from Grændalur evidence for autotrophic growth of Nitrosopumilus-like Thaumarchaea, likely coupled to am­monia oxidation, was collected (chapter 5). Additionally, the results strongly sug­gested a syntrophic association between the autotrophically growing Thaumar­chaea and nitrite-oxidizing bacteria (NOB) of the Nitrospira sublineages I and II. The work of chapter 5 furthermore showed that the autotrophically active nitrifiers in this soil (i.e. Thaumarchaea and Nitrospira-like NOB) are stimulated by application of inorganic N in form of ammonium, but suppressed by the pres­ence of active methane-oxidizing bacteria (MOB). Likely, this negative interac­tion is a result of competition for common resources like inorganic N and oxygen. Intriguingly, growth of the total Thaumarchaeal community did not seize under conditions of suppressed net nitrification and autotrophic growth. In addition, the Thaumarchaeal community structure did not change. The data collected in this thesis therefore sug­gests that at least some Thaumarchaea possess the metabolic plasticity to choose for an energetically more advantageous mode of growth than lithoautotrophy by growing mixotrophically, possibly in association with mineralizers (chapters 3 and 5)

Methyl fluoride affects methanogenesis rather than community composition of methanogenic archaea in a rice field soil

The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH3F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH3F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH3F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH3F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH3F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens

AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox nitrospira in the environment

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers (“comammox”), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems

Amplicon sequencing of genus Nitrospira from nine Austrian saline-alkaline lakes

To portray Nitrospira distribution, diversity, functionality, and adaptation in an extreme natural system we studied hypo- and subsaline, highly alkaline (pH 8.5-9.8) lakes of the Austrian national park “Neusiedler See-Seewinkel” by amplicon sequencing. Our results show surprisingly diverse Nitrospira populations from lineages I, II and IV inhabiting lake sediments with high alkalinity and elevated salinity and indicate a strong competitive advantage of Nitrospira lineage IV members at high pH