Ralf Conrad

University of the Republic, Uruguay, Montevideo, Departamento de Montevideo, Uruguay

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Publications (368)1381.79 Total impact

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    ABSTRACT: We have known for 40 years that soils can consume the trace amounts of molecular hydrogen (H2) found in the Earth's atmosphere. This process is predicted to be the most significant process in the global hydrogen cycle. However, the organisms and enzymes responsible for this process were only recently identified. Pure culture experiments demonstrated that several species of Actinobacteria, including streptomycetes and mycobacteria, can couple the oxidation of atmospheric H2 to the reduction of ambient O2. A combination of genetic, biochemical, and phenotypic studies suggest that these organisms primarily use this fuel source to sustain electron input into the respiratory chain during energy-starvation. This process is mediated by a specialized enzyme, the Group 5 [NiFe]-hydrogenase, which is unusual for its high-affinity, oxygen-insensitivity, and thermostability. Atmospheric hydrogen scavenging is a particularly dependable mode of energy-generation, given both the ubiquity of the substrate and the stress-tolerance of its catalyst. This review summarizes the recent progress in understanding how and why certain organisms scavenge atmospheric H2. In addition, it provides insight into the wider significance of hydrogen scavenging in global H2 cycling and soil microbial ecology. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
    Applied and Environmental Microbiology 12/2014; · 3.95 Impact Factor
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    ABSTRACT: Archaea are widespread and abundant in many terrestrial and aquatic environments, and are thus outside extreme environments, accounting for up to ~10% of the prokaryotes. Compared to bacteria and other microorganisms, however, very little is known about the abundance, diversity, and dispersal of archaea in the atmosphere. By means of DNA analysis and Sanger sequencing targeting the 16S rRNA (435 sequences) and amoA genes in samples of air particulate matter collected over 1 year at a continental sampling site in Germany, we obtained first insights into the seasonal dynamics of airborne archaea. The detected archaea were identified as Thaumarchaeota or Euryarchaeota, with soil Thaumarchaeota (group I.1b) being present in all samples. The normalized species richness of Thaumarchaeota correlated positively with relative humidity and negatively with temperature. This together with an increase in bare agricultural soil surfaces may explain the diversity peaks observed in fall and winter. The detected Euryarchaeota were mainly predicted methanogens with a low relative frequency of occurrence. A slight increase in their frequency during spring may be linked to fertilization processes in the surrounding agricultural fields. Comparison with samples from the Cape Verde islands (72 sequences) and from other coastal and continental sites indicates that the proportions of Euryarchaeota are enhanced in coastal air, which is consistent with their suggested abundance in marine surface waters. We conclude that air transport may play an important role in the dispersal of archaea, including assumed ammonia-oxidizing Thaumarchaeota and methanogens.
    Biogeosciences 11/2014; 11:6067-6079. · 3.75 Impact Factor
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    ABSTRACT: Sampling strategy is important for unbiased analysis of the characteristics of microbial communities in the environment. During field work it is not always possible to analyze fresh samples immediately or store them frozen. Therefore, the effect of short-term storage temperature was investigated on the abundance and composition of bacterial, archaeal and denitrifying communities in environmental samples from two different sampling sites. Oxic forest soil and anoxic pond sediment were investigated by measuring microbial abundance (DNA) and transcriptional activity (RNA). Prior to investigating the effect of storage temperature, samples were immediately analyzed, in order to represent the original situation in the habitat. The effect of storage temperature was then determined after 11 days at different low temperatures (room temperature, 4 °C, −22 °C and −80 °C). Community profiling using terminal restriction fragment length polymorphism (T-RFLP) showed no significant differences between the immediately analyzed reference sample and the samples stored at different incubation temperatures, both for DNA and RNA extracts. The abundance of microbial communities was determined using quantitative PCR and it also revealed a stable community size at all temperatures tested. By contrast, incubation at an elevated temperature (37 °C) resulted in changed bacterial community composition. In conclusion, short-term storage, even at room temperature, did not affect microbial community composition, abundance and transcriptional activity in aerated forest soil and anoxic pond sediment.
    Systematic and Applied Microbiology 11/2014; · 3.31 Impact Factor
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    ABSTRACT: The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.
    PLoS ONE 10/2014; 9(10):e110128. · 3.53 Impact Factor
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    ABSTRACT: The methane emitted from rice fields originates to a large part (up to 60%) from plant photosynthesis and is formed on the rice roots by methanogenic archaea. To investigate to which extent root colonization controls CH4 emission, we pulse-labeled rice microcosms with 13CO2 to determine the rates of 13CH4 emission exclusively derived from photosynthates. We also measured emission of total CH4 (12+13CH4), which was largely produced in the soil. The total abundances of archaea and methanogens on the roots and in the soil were analyzed by quantitative PCR of the archaeal 16S rRNA gene and the mcrA gene coding for a subunit of the methyl coenzyme M reductase, respectively. The composition of archaeal and methanogenic communities was determined with terminal restriction fragment length polymorphism (T-RFLP). During the vegetative growth stages, emission rates of 13CH4 linearly increased with the abundance of methanogenic archaea on the roots and then decreased during the last plant growth stage. Rates of 13CH4 emission and the abundance of methanogenic archaea were lower when the rice was grown in quartz-vermiculite with only 10% rice soil. Rates of total CH4 emission were not systematically related to the abundance of methanogenic archaea in soil plus roots. The composition of the archaeal communities was similar under all conditions; however, the analysis of mcrA genes indicated that the methanogens differed between the soil and root. Our results support the hypothesis that rates of photosynthesis-driven CH4 emission are limited by the abundance of methanogens on the roots.
    Environmental Microbiology 10/2014; · 6.24 Impact Factor
  • Jörn Penger, Ralf Conrad, Martin Blaser
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    ABSTRACT: Temperature is the major driving force for many biological as well as chemical reactions and may impact the fractionation of stable carbon isotopes. Thus, a good correlation between temperature and fractionation is observed in many chemical systems that are controlled by an equilibrium isotope effect. In contrast, biological systems that are usually controlled by a kinetic isotope effect are less well studied with respect to temperature effects and have shown contrasting results. We studied three different biological pathways (methylotrophic methanogenesis, hydrogenotrophic methanogenesis, acetogenesis by the acetyl-CoA pathway) which are characterized by very strong carbon isotope enrichment factors (−50‰ to −83‰). The microorganisms (Methanosarcina barkeri, Methanosarcina acetivorans, Methanolobus zinderi, Methanothermobacter marburgensis, Methanothermobacter thermoautotrophicus, Thermoanaerobacter kivui) exhibiting these pathways were grown at different temperatures ranging between 25 and 68 °C, and the fractionation factors were determined from 13C/12C isotope discrimination during substrate depletion and product formation. Our experiments showed that the fractionation factors were different for the different metabolic pathways but were not much affected by the different growth temperatures. Slight variations were well within the standard errors of replication and regression analysis. Our results showed that temperature had no significant effect on the fractionation of stable carbon isotopes during anaerobic microbial metabolism with relatively strong isotope fractionation.
    Geochimica et Cosmochimica Acta 09/2014; 140:95–105. · 4.25 Impact Factor
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    ABSTRACT: In anoxic environments, degradation of organic matter (OM) results in strong fractionation of carbon isotopes, with formation of 13C-depleted CH4. Propionate and acetate are important products of OM fermentation. Propionate is further fermented to acetate. Acetate is a direct precursor of CH4, the remainder usually being produced from H2-mediated CO2 reduction. There is a paucity of data for the turnover of acetate and, even more so, propionate. We therefore analyzed the δ13C values of organic carbon, propionate, acetate and the methyl (Me) group of acetate (acetate-Me) during the production of CH4 in anoxic incubations of various flooded and non-flooded soils and various lake sediments. Incubation in the presence of methylfluoride (CH3F), which inhibits CH4 production from acetate, allowed exclusion of isotope effects during aceticlastic methanogenesis. Despite the variation inherent in the wide diversity of sample type and origin, the data collectively showed that the δ13C value of acetate was only marginally different (-2 ± 5‰) from that of OM, while propionate was depleted in 13C relative to total acetate (-6 ± 5‰). Acetate-Me was generally depleted in 13C relative to total acetate (-8 ± 5‰). Thus, isotopic enrichment factors during the degradation of OM to total propionate and acetate were much smaller than those during hydrogenotrophic and aceticlastic methanogenesis or the intramolecular difference in δ13C between the carboxyl (CO2H) and Me of acetate, so that the δ13C value of OM may be used as a proxy when data for acetate are not available.
    Organic Geochemistry 08/2014; 73:1-7. · 2.83 Impact Factor
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    ABSTRACT: Oxygen availability is a major factor and evolutionary force determining the metabolic strategy of bacteria colonizing an environmental niche. In the soil, conditions can switch rapidly between oxia and anoxia, forcing soil bacteria to remodel their energy metabolism accordingly. Mycobacterium is a dominant genus in the soil, and all its species are obligate aerobes. Here we show that an obligate aerobe, the soil actinomycete Mycobacterium smegmatis, adopts an anaerobe-type strategy by activating fermentative hydrogen production to adapt to hypoxia. This process is controlled by the two-component system DosR-DosS/DosT, an oxygen and redox sensor that is well conserved in mycobacteria. We show that DosR tightly regulates the two [NiFe]-hydrogenases: Hyd3 (MSMEG_3931-3928) and Hyd2 (MSMEG_2719-2718). Using genetic manipulation and high-sensitivity GC, we demonstrate that Hyd3 facilitates the evolution of H2 when oxygen is depleted. Combined activity of Hyd2 and Hyd3 was necessary to maintain an optimal NAD+/NADH ratio and enhanced adaptation to and survival of hypoxia. We demonstrate that fermentatively-produced hydrogen can be recycled when fumarate or oxygen become available, suggesting Mycobacterium smegmatis can switch between fermentation, anaerobic respiration, and aerobic respiration. Hydrogen metabolism enables this obligate aerobe to rapidly meet its energetic needs when switching between microoxic and anoxic conditions and provides a competitive advantage in low oxygen environments.
    Proceedings of the National Academy of Sciences 07/2014; · 9.81 Impact Factor
  • Yucheng Wu, Ralf Conrad
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    ABSTRACT: Accumulating evidence suggests that thaumarchaeota may control nitrification in acidic soils. However, the composition of the thaumarchaeotal communities and their functioning is not well known. Therefore, we studied nitrification activity in relation to abundance and composition of thaumarchaeota in an acidic red soil from China, using microcosms incubated with and without cellulose amendment. Cellulose was selected to simulate the input of crop residues used to increase soil fertility by local farming. Accumulation of NO3--N was correlated with the growth of thaumarchaeota as determined by qPCR of 16S rRNA and ammonia monooxygenase (amoA) genes. Both nitrification activity and thaumarchaeotal growth were inhibited by acetylene. They were also inhibited by cellulose amendment, possibly due to the depletion of ammonium by enhanced heterotrophic assimilation. These results indicated that growth of thaumarchaeota was dependent on ammonia oxidation. The thaumarchaeotal 16S rRNA gene sequences in the red soil were dominated by a clade related to soil fosmid clone 29i4 within the group I.1b, which is widely distributed but so far uncultured. The archaeal amoA sequences were mainly related to the Nitrososphaera sister cluster. These observations suggest that fosmid clone 29i4 and Nitrososphaera sister cluster represent the same group of thaumarchaeota, and dominate ammonia oxidation in acidic red soil.This article is protected by copyright. All rights reserved.
    FEMS Microbiology Ecology 04/2014; · 3.88 Impact Factor
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    ABSTRACT: In the Earth's lower atmosphere, H2 is maintained at trace concentrations (0.53 ppmv/0.40 nM) and rapidly turned over (lifetime ≤ 2.1 y(-1)). It is thought that soil microbes, likely actinomycetes, serve as the main global sink for tropospheric H2. However, no study has ever unambiguously proven that a hydrogenase can oxidize this trace gas. In this work, we demonstrate, by using genetic dissection and sensitive GC measurements, that the soil actinomycete Mycobacterium smegmatis mc(2)155 constitutively oxidizes subtropospheric concentrations of H2. We show that two membrane-associated, oxygen-dependent [NiFe] hydrogenases mediate this process. Hydrogenase-1 (Hyd1) (MSMEG_2262-2263) is well-adapted to rapidly oxidize H2 at a range of concentrations [Vmax(app) = 12 nmol⋅g⋅dw(-1)⋅min(-1); Km(app) = 180 nM; threshold = 130 pM in the Δhyd23 (Hyd1 only) strain], whereas Hyd2 (MSMEG_2719-2720) catalyzes a slower-acting, higher-affinity process [Vmax(app) = 2.5 nmol⋅g⋅dw(-1)⋅min(-1); Km(app) = 50 nM; threshold = 50 pM in the Δhyd13 (Hyd2 only) strain]. These observations strongly support previous studies that have linked group 5 [NiFe] hydrogenases (e.g., Hyd2) to the oxidation of tropospheric H2 in soil ecosystems. We further reveal that group 2a [NiFe] hydrogenases (e.g., Hyd1) can contribute to this process. Hydrogenase expression and activity increases in carbon-limited cells, suggesting that scavenging of trace H2 helps to sustain dormancy. Distinct physiological roles for Hyd1 and Hyd2 during the adaptation to this condition are proposed. Soil organisms harboring high-affinity hydrogenases may be especially competitive, given that they harness a highly dependable fuel source in otherwise unstable environments.
    Proceedings of the National Academy of Sciences 03/2014; · 9.81 Impact Factor
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    ABSTRACT: Ammonia oxidation, performed by specialized microorganisms belonging to the Bacteria and Archaea, is the first and most limiting step of soil nitrification. Nitrification has not yet been examined in young volcanic soils. The aim of the present work was to evaluate the abundance and diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in acidic volcanic soils (andisols) of different defined ages to determine their relative contribution to nitrification and soil colonization. Soil was collected from three vegetated sites on Llaima Volcano (Chile) recolonized after lava eruptions in 1640, 1751 and 1957. Quantitative polymerase chain reaction, terminal restriction fragment length polymorphism and clone sequence analyses of the amoA gene were performed for the AOA and AOB communities. All soils showed high nitrification potentials, but they were highest in the younger soils. Archaeal amoA genes outnumbered bacterial amoA genes at all sites, and AOA abundances were found to be proportional to the nitrification potentials. Sequencing indicated the presence of AOA related to Nitrososphaera and Nitrosotalea, and AOB related primarily to Nitrosospira and sporadically to Nitrosomonas. The study showed that both AOA and AOB are early colonizers of andisols, but that AOA outnumber AOB and play an important role in nitrification.
    Environmental Microbiology Reports 02/2014; 6(1):70-9. · 3.26 Impact Factor
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    ABSTRACT: Methanogenic microbial communities in soil and sediment function only when the environment is inundated and anoxic. In contrast to submerged soils, desiccation of lake sediments happens only rarely. However, some predictions suggest that extreme events of drying will become more common in the Amazon region, and this will promote an increase in sediments drying and exposure. We asked whether and how such methanogenic communities can withstand desiccation stress. Therefore, we determined the rates and pathways of CH4 production (analysis of CH4 and δ(13) C of CH4 , CO2 and acetate), the copy numbers of bacterial and archaeal 16S rRNA genes and mcrA genes (quantitative PCR), and the community composition of Archaea and Bacteria (T-RFLP and pyrosequencing) in oxbow lake sediments of rivers in the Brazilian Amazon region. The rivers were of white water, black water and clear water type. The measurements were done with sediment in fresh state and after drying and rewetting. After desiccation and rewetting the composition of both, the archaeal and bacterial community changed. Since lake sediments from white water rivers exhibited only negligible methanogenic activity, probably because of relatively high iron and low organic matter content, they were not further analysed. The other sediments produced CH4 , with hydrogenotrophic methanogenesis usually accounting for > 50% of total activity. After desiccation and rewetting, archaeal and bacterial gene copy numbers decreased. The bacterial community showed a remarkable increase of Clostridiales from about 10% to > 30% of all Bacteria, partially caused by proliferation of specific taxa as the numbers of OTU shared with fresh sediment decreased from about 9% to 3%. Among the Archaea, desiccation specifically enhanced the relative abundance of either Methanocellales (black water) and/or Methanosarcinaceae (clear water). Despite the changes in gene copy numbers and composition of the microbial community, rates of CH4 production even increased after desiccation-rewetting, demonstrating that the function of the methanogenic microbial community had not been impaired. This result indicates that the increase in extreme events of drying may increase methane production in flooded sediments.
    Environmental Microbiology 09/2013; · 6.24 Impact Factor
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    Xiubin Ke, Yahai Lu, Ralf Conrad
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    ABSTRACT: Archaea in rice fields play an important role in carbon and nitrogen cycling. They comprise methane-producing Euryarchaeota as well as ammonia-oxidizing Thaumarchaeota, but their community structures and population dynamics have not yet been studied in the same system. Different soil compartments (surface, bulk, rhizospheric soil) and ages of roots (young and old roots) at two N fertilization levels and at three time points (the panicle initiation, heading and maturity periods) of the season were assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of archaeal genes (mcrA, amoA, 16S rRNA). The community of total Archaea in soil and root samples mainly consisted of the methanogens and the Thaumarchaeota and their abundance increased over the season. Methanogens proliferated everywhere, but Thaumarchaeota only on the roots and in response to nitrogen fertilization. The community structures of Archaea, methanogens and Thaumarchaeota, were different in soil and root samples indicating niche differentiation. While Methanobacteriales were generally present, Methanosarcinaceae and Methanocellales were the dominant methanogens in soil and root samples, respectively. The results emphasize the specific colonization of roots by two ecophysiologically different groups of archaea which may belong to the core root biome. This article is protected by copyright. All rights reserved.
    FEMS Microbiology Ecology 08/2013; · 3.88 Impact Factor
  • Q. Yuan, J. Pump, R. Conrad
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    ABSTRACT: Flooded rice fields are an important source of the greenhouse gas methane. Methane is produced from rice straw (RS), soil organic matter (SOM), and rice root organic carbon (ROC). Addition of RS is widely used for ameliorating soil fertility. However, this practice provides additional substrate for CH4 production and results in increased CH4 emission. Here, we found that decomposing RS is not only a substrate of CH4 production, but in addition stimulates CH4 production from SOM and ROC. Apart from accelerating the creation of reduced conditions in the soil environment, RS decomposition exerted a positive priming effect on SOM-derived CH4 production. In particular, hydrogenotrophic methanogenesis from SOM-derived CO2 was stimulated, presumably by H2 released from RS decomposition. On the other hand, the positive priming effect of RS on ROC-derived CH4 production was probably caused by the significant increase of the abundance of methanogenic archaea in the RS treatment compared with the untreated control. Our results show that traditional management of rice residues exerts a positive feedback on CH4 production from rice fields, thus exacerbating its effect on the global CH4 budget.
    Biogeosciences Discussions 08/2013; 10(8):14169-14193.
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    Ke Ma, Ralf Conrad, Yahai Lu
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    ABSTRACT: The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (T-RFLP) and abundance (qPCR) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA was relatively low, but was significantly stimulated by drainage. However, in the rhizosphere and surface soils it was the opposite, as potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (to less extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded condition. Drainage affected the composition of methanotrophic community only little, but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in abundance, composition, and activity of the various type I and type II methanotrophs both on a seasonal and spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere.
    Applied and Environmental Microbiology 06/2013; · 3.95 Impact Factor
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    ABSTRACT: The relationship between total and metabolically active soil microbial communities can change drastically with environment. In drylands, water availability is a key factor limiting cells' activity. We surveyed the diversity of total and active archaea and bacteria in soils ranging from arid desert to Mediterranean forests. Thirty composited soil samples were retrieved from five sites along a precipitation gradient, collected from patches located between and under the dominant perennial plant at each site. Molecular fingerprinting was used to site-sort the communities according of their 16S rRNA genes (total community) and their rRNA (active community) amplified by PCR or RT-PCR from directly extracted soil nucleic acids. The differences between soil samples were much higher in total rather than active microbial communities: differences in DNA fingerprints between sites were 1.2 and 2.5 times higher than RNA differences (for archaea and bacteria, respectively). Patch-type discrepancies between DNA fingerprints were on average 2.7 to 19.7 times greater than RNA differences. Moreover, RNA-based community patterns were highly correlated with soil moisture but did not necessarily follow spatial distribution pattern. Our results suggest that in water-limited environments, the spatial patterns obtained by analysis of active communities are not as robust as those drawn from total communities. This article is protected by copyright. All rights reserved.
    FEMS Microbiology Ecology 06/2013; · 3.88 Impact Factor
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    ABSTRACT: [1] Lakes are a significant source of atmospheric CH4 and play an important role in the global carbon cycle. Little information on methane production in high-altitude lakes is available. We determined the methanogenic archaeal community composition, the methanogenic pathways, and carbon isotope fractionation in lake sediments and wetland soils on the Tibetan Plateau at about 4000 m above sea level (asl). We measured CH4 production rates and the δ13C of CO2, CH4, and acetate in the presence and absence of methyl fluoride, an inhibitor of acetotrophic methanogenesis, in sediments of five lakes (Awong Co, Bangong Co, Gongzhu Co, Daze Co, and Ranwu) and wetland soils adjacent to Bangong Co and Ranwu. Methane in Bangong Co sediment and in the wetland soil near Ranwu was mainly produced by acetotrophic methanogenesis, whereas methane in the sediments of the two saline lakes Awong Co and Gongzhu Co was mainly generated by hydrogenotrophic methanogensis; chemolithotrophic acetogenesis and methanol-dependent methanogenesis may also have played a role. The stable carbon isotope fractionation during CH4 production from CO2 was relatively large (average ε = −78‰). The methanogenic communities were similar to those found in lowland lake sediments, but those of saline and nonsaline Tibetan lakes differed. Hydrogenotrophic methanogens were dominant in lake sediments, while acetotrophic methanogens were dominant in wetland soils. Our results revealed diversity in the methanogenic communities and their methanogenic pathways and indicated that they are affected by sediment characteristics, such as salinity. However, the CH4 production rates ranging from 6 to 122 nmol day−1 g dry weight−1 showed no relationship to environmental characteristics and were not limited by microbial abundance.
    Journal of Geophysical Research: Biogeosciences 06/2013; 118(2). · 3.02 Impact Factor
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    ABSTRACT: Irrigated rice fields in Uruguay are temporarily established on soils used as cattle pastures. Typically, 4 years of cattle pasture are alternated with 2 years of irrigated rice cultivation. Thus, oxic upland conditions are rotated with seasonally anoxic wetland conditions. Only the latter conditions are suitable for the production of CH4 from anaerobic degradation of organic matter. We studied soil from a permanent pasture as well as soils from different years of the pasture-rice rotation hypothesizing that activity and structure of the bacterial and archaeal communities involved in production of CH4 change systematically with the duration of either oxic or anoxic conditions. Soil samples were taken from drained fields, air-dried and used for the experiments. Indeed, methanogenic archaeal gene copy numbers (16S rRNA, mcrA) were lower in soil from the permanent pasture than from the pasture-rice alternation fields, but within the latter, there was no significant difference. Methane production started to accumulate after 16 days and 7 days of anoxic incubation in soil from the permanent pasture and the pasture-rice alternation fields respectively. Then, CH4 production rates were slightly higher in the soils used for pasture than for rice production. Analysis of δ(13) C in CH4 , CO2 and acetate in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis, indicated that CH4 was mainly (58-75%) produced from acetate, except in the permanent pasture soil (42%). Terminal restriction fragment length polymorphism (T-RFLP) of archaeal 16S rRNA genes showed no difference among the soils from the pasture-rice alternation fields with Methanocellaceae and Methanosarcinaceae as the main groups of methanogens, but in the permanent pasture soil, Methanocellaceae were relatively less abundant. T-RFLP analysis of bacterial 16S rRNA genes allowed the distinction of permanent pasture and fields from the pasture-rice rotation, but nevertheless with a high similarity. Pyrosequencing of bacterial 16S rRNA genes generally revealed Firmicutes as the dominant bacterial phylum, followed by Proteobacteria, Acidobacteria and Actinobacteria. We conclude that a stable methanogenic microbial community established once pastures have been turned into management by pasture-rice alternation despite the fact that 2 years of wetland conditions were followed by 4 years of upland conditions that were not suitable for CH4 production.
    Environmental Microbiology 05/2013; · 6.24 Impact Factor
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    Roey Angel, Ralf Conrad
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    ABSTRACT: Biological soil crusts (biocrusts) are photosynthetic mats formed through an association of prokaryotic and eukaryotic microorganisms with soil particles. Biocrusts are found in virtually any terrestrial ecosystem where vascular plant coverage is abiotically limited, with drylands comprising the primary habitat for them. We studied the dynamics of the active bacterial community in two biocrusts from an arid and a hyperarid region in the Negev Desert, Israel, under light-oxic and dark-anoxic incubation conditions after simulated rainfall. We used H2 (18) O for hydrating the crusts and analysed the bacterial community in the upper and lower parts of the biocrust using an RNA-stable isotope probing approach coupled with 454-pyrosequencing. In both biocrusts, two distinct bacterial communities developed under each incubation condition. The active anaerobic communities were initially dominated by members of the order Bacillales which were later replaced by Clostridiales. The aerobic communities on the other hand were dominated by Sphingobacteriales and several Alphaproteobacteria (Rhizobiales, Rhodobacterales, Rhodospirillales and Rubrobacteriales). Actinomycetales were the dominant bacterial order in the dry crusts but quickly collapsed and accounted for < 1% of the community by the end of the incubation. Our study shows that biocrusts host a diverse community whose members display complex interactions as they resuscitate from dormancy.
    Environmental Microbiology 04/2013; · 6.24 Impact Factor

Publication Stats

15k Citations
1,381.79 Total Impact Points


  • 2013
    • University of the Republic, Uruguay
      • Departamento de Biociencias
      Montevideo, Departamento de Montevideo, Uruguay
  • 2005–2013
    • China Agricultural University
      • College of Resources and Environmental Sciences
      Beijing, Beijing Shi, China
  • 2000–2013
    • Max Planck Institute for Terrestrial Microbiology
      • Department of Biogeochemistry
      Marburg, Hesse, Germany
  • 2003–2012
    • Russian Academy of Sciences
      • Institute of Microbiology
      Moskva, Moscow, Russia
  • 2011
    • Chinese Academy of Sciences
      Peping, Beijing, China
  • 1992–2011
    • Max Planck Institute for Marine Microbiology
      Bremen, Bremen, Germany
  • 2010
    • Federal University of Rio de Janeiro
      • Instituto de Biologia (IB)
      Rio de Janeiro, Rio de Janeiro, Brazil
    • Northeast Institute of Geography and Agroecology
      • Institute of Soil Science
      Beijing, Beijing Shi, China
  • 2009
    • Hainan University
      Haikou, Yunnan, China
  • 2008
    • Siberian Federal University
      Красноярск, Krasnoyarskiy, Russia
  • 2007
    • Bundesanstalt für Materialforschung und -prüfung
      Berlín, Berlin, Germany
    • Helmholtz Centre for Infection Research
      Brunswyck, Lower Saxony, Germany
    • The University of Tokyo
      • Department of Biotechnology
      Edo, Tōkyō, Japan
  • 1996–2007
    • Philipps University of Marburg
      Marburg, Hesse, Germany
  • 2006
    • Leibniz-Institute of Freshwater Ecology and Inland Fisheries
      Berlín, Berlin, Germany
    • Freie Universität Berlin
      Berlín, Berlin, Germany
    • Netherlands Institute of Ecology (NIOO-KNAW)
      Wageningen, Gelderland, Netherlands
  • 1979–2006
    • Max Planck Institute for Chemistry
      Mayence, Rheinland-Pfalz, Germany
  • 2004
    • Justus-Liebig-Universität Gießen
      • Institut für Angewandte Mikrobiologie
      Gießen, Hesse, Germany
  • 1986–1993
    • Universität Konstanz
      Constance, Baden-Württemberg, Germany
  • 1985–1988
    • University of Wisconsin, Madison
      • Department of Bacteriology
      Madison, MS, United States