TY - JOUR A1 - Shrestha, M. A1 - Abraham, W.-R. A1 - Shrestha, P.M. A1 - Noll, Matthias A1 - Conrad, R. T1 - Activity and composition of methanotrophic bacterial communities in planted rice soil studied by flux measurements, analyses of pmoA gene and stable isotope probing of phospholipid fatty acids N2 - Methanotrophs in the rhizosphere of rice field ecosystems attenuate the emissions of CH4 into the atmosphere and thus play an important role for the global cycle of this greenhouse gas. Therefore, we measured the activity and composition of the methanotrophic community in the rhizosphere of rice microcosms. Methane oxidation was determined by measuring the CH4 flux in the presence and absence of difluoromethane as a specific inhibitor for methane oxidation. Methane oxidation started on day 24 and reached the maximum on day 32 after transplantation. The total methanotrophic community was analysed by terminal restriction fragment length polymorphism (T-RFLP) and cloning/sequencing of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. The metabolically active methanotrophic community was analysed by stable isotope probing of microbial phospholipid fatty acids (PLFA-SIP) using 13C-labelled CH4 directly added to the rhizospheric region. Rhizospheric soil and root samples were collected after exposure to 13CH4 for 8 and 18 days. Both T-RFLP/cloning and PLFA-SIP approaches showed that type I and type II methanotrophic populations changed over time with respect to activity and population size in the rhizospheric soil and on the rice roots. However, type I methanotrophs were more active than type II methanotrophs at both time points indicating they were of particular importance in the rhizosphere. PLFA-SIP showed that the active methanotrophic populations exhibit a pronounced spatial and temporal variation in rice microcosms. KW - Methane oxidation KW - Active methanotrophs KW - Rice microcosms KW - PLFA KW - pmoA gene PY - 2008 DO - https://doi.org/10.1111/j.1462-2920.2007.01462.x SN - 1462-2912 SN - 1462-2920 VL - 10 IS - 2 SP - 400 EP - 412 PB - Blackwell Science CY - Oxford AN - OPUS4-16493 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Qiu, Q. A1 - Noll, Matthias A1 - Abraham, W.-R. A1 - Lu, Y. A1 - Conrad, R. T1 - Applying stable isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field to study activity and composition of the methanotrophic bacterial communities in situ N2 - Methanotrophs in the rhizosphere play an important role in global climate change since they attenuate methane emission from rice field ecosystems into the atmosphere. Most of the CH4 is emitted via transport through the plant gas vascular system. We used this transport for stable isotope probing (SIP) of the methanotrophs in the rhizosphere under field conditions and pulse-labelled rice plants in a Chinese rice field with CH4 (99% 13C) for 7 days. The rate of 13CH4 loss rate during 13C application was comparable to the CH4 oxidation rate measured by the difluoromethane inhibition technique. The methanotrophic communities on the roots and in the rhizospheric soil were analyzed by terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing of the particulate methane monooxygenase (pmoA) gene. Populations of type I methanotrophs were larger than those of type II. Both methane oxidation rates and composition of methanotrophic communities suggested that there was little difference between urea-fertilized and unfertilized fields. SIP of phospholipid fatty acids (PLFA-SIP) and rRNA (RNA-SIP) were used to analyze the metabolically active methanotrophic community in rhizospheric soil. PLFA of type I compared with type II methanotrophs was labelled more strongly with 13C, reaching a maximum of 6.8 atom-% . T-RFLP analysis and cloning/sequencing of 16S rRNA genes showed that methanotrophs, especially of type I, were slightly enriched in the 'heavy' fractions. Our results indicate that CH4 oxidation in the rice rhizosphere under in situ conditions is mainly due to type I methanotrophs. KW - Methane-oxidizing bacteria KW - Rice field KW - Rhizosphere KW - Stable isotope probing KW - Phospholipid fatty acid KW - Particulate methane monooxygenase PY - 2008 DO - https://doi.org/10.1038/ismej.2008.34 SN - 1751-7362 SN - 1751-7370 IS - 2 SP - 602 EP - 614 PB - Nature Publishing Group CY - Basingstoke AN - OPUS4-17660 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Moldovan, R.-P. A1 - Wenzel, B. A1 - Teodoro, R. A1 - Neumann, W. A1 - Dukic-Stefanovic, S. A1 - Kraus, Werner A1 - Rong, P. A1 - Deuther-Conrad, W. A1 - Hey-Hawkins, E. A1 - Krügel, U. A1 - Brust, P. T1 - Studies towards the development of a PET radiotracer for imaging of the P2Y1 receptors in the brain: synthesis, 18F-labeling and preliminary biological evaluation N2 - Purine nucleotides such as ATP and ADP are important extracellular signaling molecules in almost all tissues activating various subtypes of purinoreceptors. In the brain, the P2Y1 receptor (P2Y1R) subtype mediates trophic functions like differentiation and proliferation, and modulates fast synaptic transmission, both suggested to be affected in diseases of the central nervous system. Research on P2Y1R is limited because suitable brain-penetrating P2Y1R-selective tracers are not yet available. Here, we describe the first efforts to develop an 18F-labeled PET tracer based on the structure of the highly affine and selective, non-nucleotidic P2Y1R allosteric modulator 1-(2-[2-(tert-butyl)phenoxy]pyridin-3-yl)-3- [4-(trifluoromethoxy)phenyl]urea (7). A small series of fluorinated compounds was developed by systematic modification of the p-(trifluoromethoxy)phenyl, the urea and the 2-pyridyl subunits of the lead compound 7. Additionally, the p-(trifluoromethoxy)phenyl subunit was substituted by carborane, a boron-rich cluster with potential applicability in boron neutron capture therapy (BNCT). By functional assays, the new fluorinated derivative 1-{2-[2-(tert-butyl)phenoxy]pyridin-3-yl}-3-[4-(2-fluoroethyl) phenyl]urea (18) was identified with a high P2Y1R antagonistic potency (IC50 ¼10 nM). Compound [18F] 18 was radiosynthesized by using tetra-n-butyl ammonium [18F]fluoride with high radiochemical purity, radiochemical yield and molar activities. Investigation of brain homogenates using hydrophilic interaction chromatography (HILIC) revealed [18F]fluoride as major radiometabolite. Although [18F]18 showed fast in vivo metabolization, the high potency and unique allosteric binding mode makes this class of compounds interesting for further optimizations and investigation of the theranostic potential as PET tracer and BNCT agent. KW - Purine P2Y1 receptors KW - Positron emission tomography KW - Brain PET tracers KW - Radiometabolites KW - Micellar chromatography KW - Hydrophilic interaction chromatography PY - 2019 DO - https://doi.org/10.1016/j.ejmech.2019.01.006 SN - 0223-5234 VL - 165 SP - 142 EP - 159 PB - Elsevier CY - Amsterdam AN - OPUS4-47253 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Conrad, R. A1 - Klose, M. A1 - Noll, Matthias A1 - Kemnitz, D. A1 - Bodelier, P.L.E. T1 - Soil type links microbial colonization of rice roots to methane emission N2 - Most of the methane (CH4) emission from rice fields is derived from plant photosynthates, which are converted to CH4. Rice cluster I (RC-1) archaea colonizing the rhizosphere were found to be the methanogens responsible for this process. Hence, RC-1 methanogens seem to play a crucial role in emission of the greenhouse gas CH4. We determined the community composition and activity of methanogens colonizing the roots of eight different rice cultivars after growth on both Italian rice soil and river bank soil, which contained different communities of methanogenic archaea. The community composition was analyzed by terminal restriction fragment length polymorphism and cloning/sequencing of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase. When grown on rice field soil, the methanogenic community of the different rice cultivars was always dominated by RC-1 methanogens. In contrast, roots were colonized by Methanomicrobiales when grown on river bank soil, in which RC-1 methanogens were initially not detectable. Roots colonized with Methanomicrobiales compared with RC-1 exhibited lower CH4 production and CH4 emission rates. The results show that the type of methanogens colonizing rice roots has a potentially important impact on the global CH4 cycle. KW - Gene sequence KW - Methane emission KW - Methanomicrobiales KW - Methyl coenzyme M reductase KW - Ribosomal RNA KW - Rice cluster I KW - Rice cultivar KW - Rice field soil KW - Rice root KW - Terminal restriction fragment length polymorphism PY - 2008 DO - https://doi.org/10.1111/j.1365-2486.2007.01516.x SN - 1354-1013 SN - 1365-2486 VL - 14 IS - 3 SP - 657 EP - 669 PB - Blackwell Science CY - Oxford AN - OPUS4-16517 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Noll, Matthias A1 - Frenzel, P. A1 - Conrad, R. T1 - Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing N2 - Methane-oxidizing bacteria (MOB) in soil are not only controlled by their main substrates, methane and oxygen, but also by nitrogen availability. We compared an unfertilized control with a urea-fertilized treatment and applied RNA-stable-isotope-probing to follow activity changes upon fertilization as closely as possible. Nitrogen fertilization of an Italian rice field soil increased the CH4 oxidation rates sevenfold. In the fertilized treatment, isopycnic separation of 13C-enriched RNA became possible after 7 days when 300 µmol 13CH4 gdry soil-1 had been consumed. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprints and clone libraries documented that the type I methanotrophic genera Methylomicrobium and Methylocaldum assimilated 13CH4 nearly exclusively. Although previous studies had shown that the same soil contains a much larger diversity of MOB, including both type I and type II, nitrogen fertilization apparently activated only a small subset of the overall diversity of MOB, type I MOB in particular. KW - Methane oxidation KW - Nitrogen fertilization KW - Urea KW - Stable isotope probing PY - 2008 DO - https://doi.org/10.1111/j.1574-6941.2008.00497.x SN - 0168-6496 SN - 1574-6941 VL - 65 IS - 1 SP - 125 EP - 132 PB - Blackwell Publishing CY - Oxford AN - OPUS4-17659 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Noll, Matthias A1 - Klose, M. A1 - Conrad, R. T1 - Effect of temperature change on the composition of the bacterial and archaeal community potentially involved in the turnover of acetate and propionate in methanogenic rice field soil N2 - The microbial community structure was investigated together with the path of methane production in Italian rice field soil incubated at moderate (35 °C) and high (45 °C) temperature using terminal restriction fragment length polymorphism and stable isotope fractionation. The structure of both the archaeal and bacterial communities differed at 35 °C compared with 45 °C, and acetoclastic and hydrogenotrophic methanogenesis dominated, respectively. Changing the incubation of the 45 °C soil to different temperatures (25, 30, 35, 40, 45, 50 °C) resulted in a dynamic change of both microbial community structure and stable isotope fractionation. In all treatments, acetate first accumulated and then decreased. Propionate was also transiently produced and consumed. It is noteworthy that acetate was also consumed at thermophilic conditions, although archaeal community composition and stable isotope fractionation indicated that acetoclastic methanogenesis did not operate. Instead, acetate must have been consumed by syntrophic acetate oxidizers. The transient accumulation and subsequent consumption of acetate at thermophilic conditions was specifically paralleled by terminal restriction fragments characteristic for clostridial cluster I, whereas those of clostridial clusters I and III, Acidaminococcaceae and Heliobacteraceae, paralleled the thermophilic turnover of both acetate and propionate. KW - Syntrophic acetate oxidation KW - Thermophilic microbial community KW - Terminal restriction fragment length polymorphism KW - Bacteria KW - Archaea KW - Structure and function KW - Methanogenic archael community KW - Temperature shift PY - 2010 DO - https://doi.org/10.1111/j.1574-6941.2010.00883.x SN - 0168-6496 SN - 1574-6941 VL - 73 IS - 2 SP - 215 EP - 225 PB - Blackwell Publishing CY - Oxford AN - OPUS4-21671 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Conrad, R. A1 - Klose, M. A1 - Noll, Matthias T1 - Functional and structural response of the methanogenic microbial community in rice field soil to temperature change N2 - The microbial community in anoxic rice field soil produces CH4 over a wide temperature range up to 55°C. However, at temperatures higher than about 40°C, the methanogenic path changes from CH4 production by hydrogenotrophic plus acetoclastic methanogenesis to exclusively hydrogenotrophic methanogenesis and simultaneously, the methanogenic community consisting of Methanosarcinaceae, Methanoseataceae, Methanomicrobiales, Methanobacteriales and Rice Cluster I (RC-1) changes to almost complete dominance of RC-1. We studied changes in structure and function of the methanogenic community with temperature to see whether microbial members of the community were lost or their function impaired by exposure to high temperature. We characterized the function of the community by the path of CH4 production measuring δ13C in CH4 and CO2 and calculating the apparent fractionation factor (αapp) and the structure of the community by analysis of the terminal restriction fragment length polymorphism (T-RFLP) of the microbial 16S rRNA genes. Shift of the temperature from 45°C to 35°C resulted in a corresponding shift of function and structure, especially when some 35°C soil was added to the 45°C soil. The bacterial community (T-RFLP patterns), which was much more diverse than the archaeal community, changed in a similar manner upon temperature shift. Incubation of a mixture of 35°C and 50°C pre-incubated methanogenic rice field soil at different temperatures resulted in functionally and structurally well-defined communities. Although function changed from a mixture of acetoclastic and hydrogenotrophic methanogenesis to exclusively hydrogenotrophic methanogenesis over a rather narrow temperature range of 42-46°C, each of these temperatures also resulted in only one characteristic function and structure. Our study showed that temperature conditions defined structure and function of the methanogenic microbial community. KW - Structure and function KW - Methanogenic archaeal community KW - Temperature shift PY - 2009 DO - https://doi.org/10.1111/j.1462-2920.2009.01909.x SN - 1462-2912 SN - 1462-2920 VL - 11 IS - 7 SP - 1844 EP - 1853 PB - Blackwell Science CY - Oxford AN - OPUS4-19596 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -