Ralf Conrad

Max Planck Institute for Terrestrial Microbiology, Marburg, Hesse, Germany

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Publications (387)1383.05 Total impact

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    ABSTRACT: Intermittent drainage is one of the most promising approaches to mitigate methane (CH4) emission from paddy fields. Irrigated rice fields in Uruguay are temporarily established on soils used as cattle pastures. We studied soil from the pasture-rice rotation (UR) as well as soil from a permanent cattle pasture (UT) hypothesizing that activity and structure of the bacterial and archaeal communities involved in production of CH4 change systematically with intermittent drainage. Methane production started after 7 days and 16 days of anoxic incubation in UR and UT soil, respectively. Then, production rates of CH4 were higher in UT than UR soil. Intermittent drainage significantly decreased the rates of CH4 production. Analysis of δ13C indicated that CH4 was mainly produced from acetate both in UR (73–98%) and UT (51–80%) soil. Intermittent drainage did not change the pathway of CH4 production. Quantitative PCR showed that methanogenic archaeal gene copy numbers (16S rRNA, mcrA) were much lower in UT than UR soil, but increased upon incubation under anoxic conditions. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing of bacterial and archaeal 16S rRNA genes showed that the communities were clearly different between UR and UT soil. The bacterial community consisted of 9 phyla with relative abundance of >1% in both soils. Whereas the archaeal community in UR soil was dominated by Methanocellales and Methanosarcinaceae, that in UT soil was dominated by Crenarchaeota. Anoxic incubation affected the composition of the bacterial and archaeal communities in UT soil, but not so much in UR soil. In UT soil, the relative abundance of Clostridiales increased to 19%, and the archaeal community changed to dominance by Methanosarcinaceae and Methanobacteriales. Subsequent drainage and re-flooding, however, had comparatively little effect on the composition, although it decreased the rates of CH4 production in both soils. Difference in previous soil management and in the structures of the microbial communities apparently only affected their dynamics and functioning after the first flooding but not upon subsequent drainage and re-flooding.
    No preview · Article · Oct 2015 · Soil Biology and Biochemistry
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    Xiubin Ke · Yahai Lu · Ralf Conrad

    Full-text · Dataset · Sep 2015
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    ABSTRACT: Crop rotation of flooded rice with upland crops is a common management scheme allowing the reduction of water consumption along with the reduction of methane emission. The introduction of an upland crop into the paddy rice ecosystem leads to dramatic changes in field conditions (oxygen availability, redox conditions). However, the impact of this practice on the archaeal and bacterial communities has scarcely been studied. Here, we provide a comprehensive study focusing on the crop rotation between flooded rice in the wet season and upland maize (RM) in the dry season in comparison to flooded rice (RR) in both seasons. The composition of the resident and active microbial communities was assessed by 454 pyrosequencing targeting the archaeal and bacterial 16S rRNA gene and 16S rRNA. The archaeal community composition changed dramatically in the rotational fields indicated by a decrease of anaerobic methanogenic lineages and an increase of aerobic Thaumarchaeota. Members of Methanomicrobiales, Methanosarcinaceae, Methanosaetaceae, Methanocellaceae were equally suppressed in the rotational fields indicating influence on both acetoclastic and hydrogenotrophic methanogens. Contrary, members of Soil Crenarchaeotic Group, mainly Candidatus Nitrososphaera, were higher in the rotational fields possibly indicating increasing importance of ammonia-oxidation during drainage. In contrast minor effects on the bacterial community were observed. Acidobacteria and Anaeromyxobacter spp. were enriched in the rotational fields while members of anaerobic Chloroflexi and sulfate reducing members of Deltaproteobacteria were found in higher abundance in the rice fields. Combining quantitative PCR and pyrosequencing data revealed increased ribosomal numbers per cell for methanogenic species during crop rotation. This stress response, however, did not allow the methanogenic community to recover in the rotational fields during re-flooding and rice cultivation. In summary, the analyses showed that crop rotation with upland maize led to dramatic changes in the archaeal community composition whereas the bacterial community was only little affected.
    No preview · Article · Sep 2015 · Environmental Microbiology
  • Xiubin Ke · Wei Lu · Ralf Conrad
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    ABSTRACT: Oxygen is considered as a limiting factor for nitrification in rice paddy soil. However, little is known about how the nitrifying microbial community responds to different oxygen concentrations at community and transcript level. In this study, soil and roots were harvested from 50-day-old rice microcosms and were incubated for up to 45 days under two oxygen concentrations: 2 % O2 and 20 % O2 (ambient air). Nitrification rates were measured from the accumulation of nitrite plus nitrate. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was determined from the abundance (using quantitative PCR (qPCR)) and composition (using terminal restriction fragment length polymorphism and cloning/sequencing) of their amoA genes, that of nitrite oxidizers (NOB) by quantifying the nxrA gene of Nitrobacter spp. and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by quantifying the copy numbers of amoA and nxrA transcripts (using RT-qPCR). Different oxygen concentrations did not affect the community compositions of AOB, AOA, and NOB, which however were different between surface soil, bottom soil, and rice roots. However, nitrification rates were higher under ambient air than 2 % O2, and abundance and transcript activities of AOB, but not of AOA, were also higher. Abundance and transcript copy numbers of Nitrobacter were also higher at ambient air. These results indicate that AOB and NOB, but not AOA, were sensitive to oxygen availability.
    No preview · Article · Jun 2015 · Microbial Ecology
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    ABSTRACT: Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet a limited number of isolates makes it difficult to understand physiology and ecological impact of the microorganisms involved. Here, two-staged cultivation was implemented to selectively enrich and isolate crystalline iron(III) reducers in soils and sediments. Firstly, iron reducers were enriched and other untargeted eutrophs were depleted by two-year successive culture on a crystalline ferric iron oxide (i.e., goethite, lepidocrocite, hematite, or magnetite) as electron acceptor. Fifty-eight out of 136 incubation conditions allowed the continued existence of microorganisms as confirmed by PCR amplification. High-throughput Illumina sequencing based on 16S rRNA genes revealed that the enrichment cultures on each of the ferric iron oxides contained bacteria belonging to the Deltaproteobacteria (mainly Geobacteraceae), followed by Firmicutes and Chloroflexi, which also comprised most of the operational taxonomic units (OTUs) identified. The Venn diagrams indicated that the core OTUs enriched with all of the iron oxides were dominant in the Geobacteraceae. Secondly, 38 enrichment cultures including novel microorganisms were transferred to soluble-iron(III) media in order to stimulate proliferation of the enriched iron reducers. Through extinction dilution-culture and single colony isolation, six strains within the Deltaproteobacteria were finally obtained; five strains belonged to the genus Geobacter and one strain to Pelobacter. These isolates had 94.8-98.1% sequence similarities of 16S rRNA genes to cultured relatives. All the isolates were able to grow on acetate and ferric iron but their physiological characteristics differed considerably in terms of growth rate. The results demonstrate the successful enrichment and isolation of novel iron(III) reducers that were able to thrive by reducing highly crystallized ferric irons.
    Full-text · Article · May 2015 · Frontiers in Microbiology
  • Dheeraj Kanaparthi · Ralf Conrad
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    ABSTRACT: Nitrate-dependent iron oxidation was discovered in 1996 and has been reported from various environments ever since. To date, despite the widespread nature of this process, all attempts to cultivate chemolithoautotrophic nitrate-dependent iron oxidizers have been unsuccessful. The present study was focused on understanding the influence of natural chelating agents of iron, like humic substances, on the culturability, activity, and enumeration, of these microorganisms. Pure culture studies conducted with Thiobacillus denitrificans showed a constant increase in cell mass with a corresponding nitrate-dependent iron oxidation activity only when Fe(II) was provided together with humic substances, compared to no growth in control incubations without humic substances. The presence of a relatively strong chelating agent, such as EDTA, inhibited the growth of Thiobacillus denitrificans. It was concluded that complex formation between humic substances and iron was required for chemolithoautotrophic nitrate-dependent iron oxidation. Most probable number enumerations showed that numbers of chemolithoautotrophic nitrate-dependent iron-oxidizing bacteria were one to three orders of magnitude higher in the presence of humic substances compared to media without. Similar results were obtained when potential nitrate-dependent iron oxidation activity was determined in soil samples. In summary, this study showed that humic substances significantly enhanced the growth and activity of autotrophic nitrate-dependent iron-oxidizing microorganisms, probably by chelation of iron. Copyright © 2015 Elsevier GmbH. All rights reserved.
    No preview · Article · Mar 2015 · Systematic and Applied Microbiology
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    ABSTRACT: Chemolithotrophic homoacetogenic bacteria apparently express a characteristic stable carbon isotope fractionation and may contribute significantly to acetate production in anoxic environments. However, fractionation factors (ε) in bacterial cultures have rarely been determined and the effect of substrate availability has not been assessed. We therefore studied the kinetic carbon isotope effect in cultures of Thermoanaerobacter kivui grown at 55 °C. The fractionation factor in HCO3- buffered medium was ca. 15‰ more negative than that in PO43- buffered medium. To test whether the difference was caused by the initial substrate ratio of H2 and total inorganic carbon (TIC; 0.5 in HCO3- vs. 4.0 in PO43- buffered medium), T. kivui was grown in either [3-(N-morpholino) propanesulfonic acid, MOPS] buffered or PO43- buffered media with different HCO3- concentration. Indeed, the fractionation factor became more negative with increasing HCO3- concentration and decreasing H2/TIC ratio. While pH had only a small effect, the fractionation was generally more negative in MOPS buffered than in phosphate buffered media, indicating that the buffer system also affected fractionation. Collectively, the results show that substrate availability and other environmental factors affect the magnitude of isotope fractionation during acetate production by chemolithotrophic homoacetogenesis.
    Full-text · Article · Feb 2015 · Organic Geochemistry
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    ABSTRACT: Microorganisms associated with the roots of plants have an important function in plant growth and in carbon sequestration in soil. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of which as root exudates that is consumed by microorganisms. A stable isotope probing (SIP) approach was used to differentiate between microorganisms using plant photosynthate or soil carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with (13)CO2 for ten days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with (13)C. 30 OTUs were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the α, β and δ classes of Proteobacteria, and the Spartobacteria and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) compared with rhizosphere (∼4%), indicating that a greater proportion of the active microbial community on the roots incorporated plant-derived carbon within the time frame of the experiment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Full-text · Article · Jan 2015 · Applied and Environmental Microbiology
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    ABSTRACT: The anoxic saccharide-rich conditions of the earthworm gut provide an ideal transient habitat for ingested microbes capable of anaerobiosis. It was recently discovered that the earthworm Eudrilus eugeniae from Brazil can emit methane (CH4) and that ingested methanogens might be associated with this emission. The objective of this study was to resolve trophic interactions of bacteria and methanogens in the methanogenic food web in the gut contents of E. eugeniae. RNA-based stable isotope probing of bacterial 16S rRNA as well as mcrA and mrtA (the alpha subunit of methyl-CoM reductase and its isoenzyme, respectively) of methanogens was performed with [(13)C]-glucose as a model saccharide in the gut contents. Concomitant fermentations were augmented by the rapid consumption of glucose, yielding numerous products, including molecular hydrogen (H2), carbon dioxide (CO2), formate, acetate, ethanol, lactate, succinate and propionate. Aeromonadaceae-affiliated facultative aerobes, and obligate anaerobes affiliated to Lachnospiraceae, Veillonellaceae and Ruminococcaceae were associated with the diverse fermentations. Methanogenesis was ongoing during incubations, and (13)C-labeling of CH4 verified that supplemental [(13)C]-glucose derived carbon was dissimilated to CH4. Hydrogenotrophic methanogens affiliated with Methanobacteriaceae and Methanoregulaceae were linked to methanogenesis, and acetogens related to Peptostreptoccocaceae were likewise found to be participants in the methanogenic food web. H2 rather than acetate stimulated methanogenesis in the methanogenic gut content enrichments, and acetogens appeared to dissimilate supplemental H2 to acetate in methanogenic enrichments. These findings provide insight on the processes and associated taxa potentially linked to methanogenesis and the turnover of organic carbon in the alimentary canal of methane-emitting E. eugeniae.The ISME Journal advance online publication, 23 January 2015; doi:10.1038/ismej.2014.262.
    No preview · Article · Jan 2015 · The ISME Journal
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    Björn Breidenbach · Ralf Conrad
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    ABSTRACT: We studied the resident (16S rDNA) and the active (16S rRNA) members of soil archaeal and bacterial communities during rice plant development by sampling three growth st ages (veget ative, reproductive and maturit y) under field conditions. Additionally, the microbial communit y was investigated in t wo non-flooded fields (unplanted, cultivated with upland maize) in order to monitor the reaction of the microbial communities to non-flooded, dr y conditions. The abundance of Bacteria and Archaea was monitored by quantit ative PCR showing an increase in 16S rDNA during reproductive st age and st able 16S rRNA copies throughout the growth season. Communit y profiling by T-RFLP indicated a relatively st able composition during rice plant growth whereas pyrosequencing revealed minor changes in relative abundance of a few bacterial groups. Comparison of the t wo non-flooded fields with flooded rice fields showed that the communit y composition of the Bacteria was slightly different, while that of the Archaea was almost the same. Only the relative abundance of Methanosarcinaceae and Soil Crenarchaeotic Group increased in non-flooded vs. flooded soil. The abundance of bacterial and archaeal 16S rDNA copies was highest in flooded rice fields, followed by non-flooded maize and unplanted fields. However, the abundance of ribosomal RNA (active microbes) was similar indicating maintenance of a high level of ribosomal RNA under the non-flooded conditions, which were unfavorable for anaerobic bacteria and methanogenic archaea. This maintenance possibly serves as preparedness for activity when conditions improve. In summary, the analyses showed that the bacterial and archaeal communities inhabiting Philippine rice field soil were relatively stable over the season but reacted upon change in field management.
    Full-text · Article · Jan 2015 · Frontiers in Microbiology
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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.
    Full-text · Article · Dec 2014 · Applied and Environmental Microbiology
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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.
    No preview · Article · Nov 2014 · Systematic and Applied Microbiology
  • Judith Pump · Ralf Conrad
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    ABSTRACT: Aims Rice fields are an important source for the greenhouse gas methane. Plants play an essential role in carbon supply for soil microbiota, but the influence of the microbial community on carbon cycling is not well understood. Methods Microcosms were prepared using sand-vermiculite amended with different soils and sediments, and planted with rice. The microcosms at different growth stages were pulse-labeled with 13CO2 followed by tracing 13C in plant, soil and atmospheric carbon pools and quantifying the abundance of methanogenic archaea in rhizosphere soil. Results Overall, >85 % of the freshly assimilated carbon was allocated in aboveground plant biomass, approximately 10 % was translocated into the roots and
    No preview · Article · Nov 2014 · Plant and Soil
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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.
    Full-text · Article · Nov 2014 · Biogeosciences
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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.
    Full-text · Article · Oct 2014 · PLoS ONE
  • Judith Pump · Jennifer Pratscher · Ralf Conrad
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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.
    No preview · Article · Oct 2014 · Environmental Microbiology
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    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.
    Full-text · Article · Sep 2014 · Geochimica et Cosmochimica Acta
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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.
    Full-text · Article · Aug 2014 · Organic Geochemistry
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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.
    Full-text · Article · Jul 2014 · Proceedings of the National Academy of Sciences
  • Sanae Sakai · Ralf Conrad · Hiroyuki Imachi
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    ABSTRACT: Methanocellaceae is a family within the order Methanocellales Sakai et al. (Int J Syst Evol Microbiol 58:929-936, 2008). This order and family contains a single genus Methanocella. Hitherto three species within the genus Methanocella have been reported Sakai et al. (Int J Syst Evol Microbiol 58:929-936, 2008; Int J Syst Evol Microbiol 60:2918-2923, 2010), Lü and Lu (PLoS ONE 7: e35279, 2012a); all the reported species were isolated from rice field soil. Cells are nonmotile, irregular rods and anaerobic; energy metabolism is by reduction of CO2 to CH4 with H2 as an electron donor; some species can also use formate as an electron donor.
    No preview · Article · Jul 2014

Publication Stats

22k Citations
1,383.05 Total Impact Points


  • 2000-2015
    • Max Planck Institute for Terrestrial Microbiology
      • Department of Biogeochemistry
      Marburg, Hesse, Germany
  • 2011
    • Government of the People's Republic of China
      Peping, Beijing, China
  • 1992-2011
    • Max Planck Institute for Marine Microbiology
      Bremen, Bremen, Germany
  • 2010
    • Chinese Academy of Sciences
      • Key Laboratory of Soil Environment and Pollution Remediation
      Peping, Beijing, China
  • 2007
    • The University of Tokyo
      • Department of Biotechnology
      Edo, Tōkyō, Japan
  • 2006-2007
    • Russian Academy of Sciences
      • Institute of Microbiology
      Moskva, Moscow, Russia
    • Leibniz-Institute of Freshwater Ecology and Inland Fisheries
      Berlín, Berlin, Germany
    • Netherlands Institute of Ecology (NIOO-KNAW)
      Wageningen, Gelderland, Netherlands
  • 1996-2007
    • Philipps University of Marburg
      Marburg, Hesse, Germany
  • 1979-2006
    • Max Planck Institute for Chemistry
      • Department of Atmospheric Chemistry
      Mayence, Rheinland-Pfalz, Germany
  • 1986-1991
    • Universität Konstanz
      Constance, Baden-Württemberg, Germany
  • 1988
    • University of Massachusetts Amherst
      • Department of Microbiology
      Amherst Center, Massachusetts, United States
  • 1984-1987
    • University of Wisconsin–Madison
      • Department of Bacteriology
      Madison, Wisconsin, United States