TY - JOUR A1 - Duc, L. A1 - Noll, Matthias A1 - Meier, B.E. A1 - Bürgmann, H. A1 - Zeyer, J. T1 - High Diversity of Diazotrophs in the Forefield of a Receding Alpine Glacier N2 - Forefields of receding glaciers are unique and sensitive environments representing natural chronosequences. In such habitats, microbial nitrogen fixation is of particular interest since the low concentration of bioavailable nitrogen is one of the key limitations for growth of plants and soil microorganisms. Asymbiotic nitrogen fixation in the Damma glacier (Swiss Central Alps) forefield soils was assessed using the acetylene reduction assay. Free-living diazotrophic diversity and population structure were resolved by assembling four NifH sequence libraries for bulk and rhizosphere soils at two soil age classes (8- and 70-year ice-free forefield). A total of 318 NifH sequences were analyzed and grouped into 45 unique phylotypes. Phylogenetic analyses revealed a higher diversity as well as a broader distribution of NifH sequences among phylogenetic clusters than formerly observed in other environments. This illustrates the importance of free-living diazotrophs and their potential contribution to the global nitrogen input in this nutrient-poor environment. NifH diversity in bulk soils was higher than in rhizosphere soils. Moreover, the four libraries displayed low similarity values. This indicated that both soil age and the presence of pioneer plants influence diversification and population structure of free-living diazotrophs. KW - Diazotrophs KW - Glacier forefield KW - Chronosequence KW - Pioneer plant KW - NifH diversity PY - 2009 DO - https://doi.org/10.1007/s00248-008-9408-5 SN - 0095-3628 SN - 1432-184X VL - 57 IS - 1 SP - 179 EP - 190 PB - Springer CY - New York, NY ; Heidelberg ; Berlin AN - OPUS4-18646 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 - 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 - 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 - Noll, Matthias A1 - Wellinger, M. T1 - Changes of the soil ecosystem along a receding glacier: Testing the correlation between environmental factors and bacterial community structure N2 - As a glacier retreats, it leaves behind it a forefield that has a natural gradient of soil formation age. We systematically sampled the Damma glacier forefield (Switzerland) along a temporal gradient of soils deglaciated between 1956 and 2002. A significant change in organic carbon content, sulfate concentration, pH, water and nucleic acid content was observed along the forefield chronosequence. Based on 16S rRNA gene based fingerprinting, the structure of the bacterial community also shifted along the forefield. Shifts in the structure of the bacterial community were significantly correlated to changes of pH, soil water content and soil age. To test the impacts of an array of environmental variables including soil age, soil water content, and different anions on the structure of the bacterial community we incubated different glacier forefield soils under specific treatment conditions for 30 days at 25 °C. The incubation of recently deglaciated soils resulted into an increase of bacteria from the family Methylocystaceae and from the class Betaproteobacteria while the community composition from matured soil changed to a lesser extent. The total nitrogen concentration in matured soil doubled during incubation, whereas the nitrogen concentrations in recently deglaciated soil stayed constant. This suggested that the microbial ecosystem functioned differently in the mature versus the recently deglaciated soils. Only soil age and soil water content could be singled out as having significant effects on the structure and composition of the bacterial community, despite the fact that bacterial communities in glacier forefields are exposed to other steep environmental gradients. KW - Alpine glacier forefield KW - Bacteria KW - Environmental explanatory variable KW - Soil age KW - Soil water content KW - Succession KW - Nitrogen KW - Inorganic anion PY - 2008 DO - https://doi.org/10.1016/j.soilbio.2008.07.012 SN - 0038-0717 VL - 40 IS - 10 SP - 2611 EP - 2619 PB - Elsevier CY - Amsterdam AN - OPUS4-17935 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Urmann, K. A1 - Schroth, M.H. A1 - Noll, Matthias A1 - Gonzalez-Gil, G. A1 - Zeyer, J. T1 - Assessment of microbial methane oxidation above a petroleum-contaminated aquifer using a combination of in situ techniques N2 - Emissions of the greenhouse gas CH4, which is often produced in contaminated aquifers, are reduced or eliminated by microbial CH4 oxidation in the overlying vadose zone. The aim of this field study was to estimate kinetic parameters and isotope fractionation factors for CH4 oxidation in situ in the vadose zone above a methanogenic aquifer in Studen, Switzerland, and to characterize the involved methanotrophic communities. To quantify kinetic parameters, several field tests, so-called gas push-pull tests (GPPTs), with CH4 injection concentrations ranging from 17 to 80 mL L-1 were performed. An apparent Vmax of 0.70 ± 0.15 mmol CH4 (L soil air)-1 h-1 and an apparent Km of 0.28 ± 0.09 mmol CH4 (L soil air)-1 was estimated for CH4 oxidation at 2.7 m depth, close to the groundwater table. At 1.1 m depth, Km (0.13 ± 0.02 mmol CH4 (L soil air)-1) was in a similar range, but Vmax (0.076 ± 0.006 mmol CH4 (L soil air)-1 h-1) was an order of magnitude lower. At 2.7 m, apparent first-order rate constants determined from a CH4 gas profile (1.9 h-1) and from a single GPPT (2.0 ± 0.03 h-1) were in good agreement. Above the groundwater table, a Vmax much higher than the in situ CH4 oxidation rate prior to GPPTs indicated a high buffer capacity for CH4. At both depths, known methanotrophic species affiliated with Methylosarcina and Methylocystis were detected by cloning and sequencing. Apparent stable carbon isotope fractionation factors a for CH4 oxidation determined during GPPTs ranged from 1.006 to 1.032. Variability was likely due to differences in methanotrophic activity and CH4 availability leading to different degrees of mass transfer limitation. This complicates the use of stable isotopes as an independent quantification method. KW - In situ quantification KW - Kinetics of microbial methane (CH4) oxidation KW - Stable isotope fractionation PY - 2008 DO - https://doi.org/10.1029/2006JG000363 SN - 0148-0227 VL - 113 SP - 02006-1-02006-11 PB - American Geophysical Union CY - Washington, DC AN - OPUS4-17332 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ferrero, Fabio A1 - Lohrer, Christian A1 - Schmidt, Bernd A1 - Noll, Matthias A1 - Malow, Marcus T1 - A mathematical model to predict the heating-up of large-scale wood piles N2 - A mathematical model to predict the heating-up in open air wood chip piles has been developed. This model includes the heat production from chemical, physical and microbial exothermal processes. In the manuscript the laboratory experiments needed to develop and validate the model are described. In addition, temperature and gas concentrations were measured in two large-scale wood piles (volumes bigger than 1000 m³), in order to provide the applicability of the model to large-scale scenarios. The predictions of the model and the large-scale experimental data showed good agreement concerning the maximum temperature reached inside an open air wood pile. Special attention has been devoted to the microbial processes, since they proved to be the most important cause of heat production in the early stages of storage. This work is intended to help in predicting and thus avoiding possible self-ignition scenarios for this type of wood storage. KW - Wood chips KW - Storage KW - Self-ignition KW - Numerical simulation KW - Large-scale piles KW - Biomass PY - 2009 DO - https://doi.org/10.1016/j.jlp.2009.02.009 SN - 0950-4230 SN - 1873-3352 VL - 22 SP - 450 EP - 459 PB - Butterworth CY - Guildford, Surrey AN - OPUS4-19200 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Weißhaupt, Petra A1 - Pritzkow, Wolfgang A1 - Noll, Matthias T1 - Nitrogen metabolism of wood decomposing basidiomycetes and their interaction with diazotrophs as revealed by IRMS N2 - Isotope ratio mass spectrometry (IRMS) is an advanced method to investigate carbon (C) and nitrogen (N) in organic samples. In particular, the N content, its isotope signature and the C/N ratio reveal important facts of nutrient cycling, niche separation and ecological food webs. In this study, the characteristics of N turnover of wood decomposing microorganisms were investigated. The growth of the white rot causing basidiomycete Trametes versicolor is enhanced after addition of ammonia or urea, whereas the brown rot causing Oligoporus placenta is not accelerated. In addition, an interaction of each fungus with atmospheric N2 assimilating (diazotrophic) bacteria was investigated. Cultivation experiments with a gas mixture of 15N2/O2 and subsequent IRMS analysis of dry biomass of the diazotrophs Azotobacter croococcum, Beijerinckia acida and Novosphingobium nitrogenifigens revealed that they assimilated up to 12% of their N from N2. The experiments reflected N availability as a prerequisite for efficient growth of decomposing basidiomycetes and diazotrophs. Fungal–bacterial co-cultivation experiments showed that depending on the growth characteristics and bacterial N2 assimilation activity N is transferred from certain bacteria into fungal biomass. Thus, the experiments gave a first indication of an interaction between wood decomposing basidiomycetes and diazotrophs, which is a novel pathway of fungal N acquisition. KW - IRMS KW - Isotope labeling KW - Microbial interaction KW - N2 assimilation KW - Nitrogen KW - Wood decomposing basidiomycetes PY - 2011 DO - https://doi.org/10.1016/j.ijms.2010.12.011 SN - 0168-1176 SN - 0020-7381 SN - 1387-3806 SN - 1873-2798 VL - 307 IS - 1-3 SP - 225 EP - 231 PB - Elsevier B.V. CY - Amsterdam AN - OPUS4-23307 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 - TY - JOUR A1 - Schmalenberger, A. A1 - Noll, Matthias T1 - Shifts in desulfonating bacterial communities along a soil chronosequence in the forefield of a receding glacier N2 - Forefields of receding glaciers are unique and sensitive environments representing natural soil chronosequences, where sulfate availability is assumed to be a limiting factor. Bacterial mineralization of organosulfur is an important sulfate-providing process in soils. We analyzed the diversity of sulfonate-desulfurizing (desulfonating) bacteria in the Damma glacier forefield on the basis of the key gene asfA by terminal restriction fragment length polymorphism and clone libraries. The community structure and sequence diversity of desulfonating bacteria differed significantly between forefield soils deglaciated in the 1990s and the 1950s. Soil age had a strong effect on the desulfonating rhizosphere communities of Agrostis rupestris, but only a slight impact on the ones from Leucanthemopsis alpina. AsfA affiliated to Polaromonas sp. was predominantly found in the more recent ice-free soils and the corresponding rhizospheres of A. rupestris, while a group of unidentified sequences was found to be dominating the matured soils and the corresponding rhizospheres of A. rupestris. The desulfonating bacterial diversity was not affected by varying levels of sulfate concentrations. The level of asfA diversity in recently deglaciated soils suggests that desulfonating bacteria are a critical factor in sulfur cycling, with defined groups dominating at different stages of soil formation. KW - AsfA KW - Sulfonate desulfurization KW - T-RFLP KW - Soil chronosequence KW - Agrostis rupestris KW - Leucanthemopsis alpina PY - 2010 DO - https://doi.org/10.1111/j.1574-6941.2009.00799.x SN - 0168-6496 SN - 1574-6941 VL - 71 IS - 2 SP - 208 EP - 217 PB - Blackwell Publishing CY - Oxford AN - OPUS4-20753 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -