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Search Results: 1 - 10 of 44866 matches for " Michael Schloter "
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The plant microbiome and its importance for plant and human health
Gabriele Berg,Martin Grube,Michael Schloter,Kornelia Smalla
Frontiers in Microbiology , 2014, DOI: 10.3389/fmicb.2014.00491
Abstract: To study plant-associated microorganisms has a long history that reaches back to Lorenz Hiltner’s definition of the rhizosphere in 1904 (Hartmann et al., 2008). Today, we know that microorganisms colonizing plant surfaces and inner tissues play an eminent role in shaping of our planet – from our natural vegetation to intense agricultural production systems up to human health. Plant-associated microorganisms have to be considered as key drivers for plant health, productivity, community composition and ecosystem functioning. For this e-book “The plant microbiome and its importance for plant and human health” we collected 18 articles, including reviews, original and opinion articles that highlight the current knowledge regarding plant microbiomes, their specificity, diversity and function as well as all aspects studying the management of plant microbiomes to improve plant performance and health. The contribution of the single articles of this research topic to these questions is discussed in detail in the mini-review and 1st chapter of the book by Berg et al., (2014a). Overall the presented articles confirm that the plant-associated microbiome has greatly expanded the metabolic repertoire of plants and often increase resource uptake and provide novel nutritional and defense pathways. Thus the plant microbiome has a direct impact on plant functional traits, such as leaf longevity, specific leaf area, leaf nutrient levels, and shoot/root ratio. By providing novel nutritional and defense pathways and by modifying biochemical pathways, the plant associated microbiome can enhance or decrease species coexistence and consequently influence not only a single plant but complete ecosystems. Thus future breeding strategies may take the importance of plant-microbe interactions more into account than in the past, to obtain plants that generate high yields and are more tolerate to the constraints of global change. Studies related to raw-eaten vegetables are a special show case in this e-book. Here the plant-associated microbiome does not only influence plant performance but strongly contributes to human health. As those microbes are also part of our diet they can either improve human health (Blaser et al., 2013) or cause heavy outbreaks of infectious diseases by transferring possible pathogens (van Oberbeck et al., 2014). Interestingly, the gathered manuscripts indicate that microbiomes of different environments are not isolated but show interplay. For example, the microbiome of vegetables, humans as well as build environment such as hospitals seems to be well-connected
Temporal Dynamics of Abundance and Composition of Nitrogen-Fixing Communities across Agricultural Soils
Michele C. Pereira e Silva, Brigitte Schloter-Hai, Michael Schloter, Jan Dirk van Elsas, Joana Falc?o Salles
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0074500
Abstract: Background Despite the fact that the fixation of nitrogen is one of the most significant nutrient processes in the terrestrial ecosystem, a thorough study of the spatial and temporal patterns in the abundance and distribution of N-fixing communities has been missing so far. Methodology/Principal Findings In order to understand the dynamics of diazotrophic communities and their resilience to external changes, we quantified the abundance and characterized the bacterial community structures based on the nifH gene, using real-time PCR, PCR-DGGE and 454-pyrosequencing, across four representative Dutch soils during one growing season. In general, higher nifH gene copy numbers were observed in soils with higher pH than in those with lower pH, but lower numbers were related to increased nitrate and ammonium levels. Results from nifH gene pyrosequencing confirmed the observed PCR-DGGE patterns, which indicated that the N fixers are highly dynamic across time, shifting around 60%. Forward selection on CCA analysis identified N availability as the main driver of these variations, as well as of the evenness of the communities, leading to very unequal communities. Moreover, deep sequencing of the nifH gene revealed that sandy soils (B and D) had the lowest percentage of shared OTUs across time, compared with clayey soils (G and K), indicating the presence of a community under constant change. Cosmopolitan nifH species (present throughout the season) were affiliated with Bradyrhizobium, Azospirillum and Methylocistis, whereas other species increased their abundances progressively over time, when appropriate conditions were met, as was notably the case for Paenibacilus and Burkholderia. Conclusions Our study provides the first in-depth pyrosequencing analysis of the N-fixing community at both spatial and temporal scales, providing insights into the cosmopolitan and specific portions of the nitrogen fixing bacterial communities in soil.
Dynamics of Soil Bacterial Communities in Response to Repeated Application of Manure Containing Sulfadiazine
Guo-Chun Ding, Viviane Radl, Brigitte Schloter-Hai, Sven Jechalke, Holger Heuer, Kornelia Smalla, Michael Schloter
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0092958
Abstract: Large amounts of manure have been applied to arable soils as fertilizer worldwide. Manure is often contaminated with veterinary antibiotics which enter the soil together with antibiotic resistant bacteria. However, little information is available regarding the main responders of bacterial communities in soil affected by repeated inputs of antibiotics via manure. In this study, a microcosm experiment was performed with two concentrations of the antibiotic sulfadiazine (SDZ) which were applied together with manure at three different time points over a period of 133 days. Samples were taken 3 and 60 days after each manure application. The effects of SDZ on soil bacterial communities were explored by barcoded pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. Samples with high concentration of SDZ were analyzed on day 193 only. Repeated inputs of SDZ, especially at a high concentration, caused pronounced changes in bacterial community compositions. By comparison with the initial soil, we could observe an increase of the disturbance and a decrease of the stability of soil bacterial communities as a result of SDZ manure application compared to the manure treatment without SDZ. The number of taxa significantly affected by the presence of SDZ increased with the times of manure application and was highest during the treatment with high SDZ-concentration. Numerous taxa, known to harbor also human pathogens, such as Devosia, Shinella, Stenotrophomonas, Clostridium, Peptostreptococcus, Leifsonia, Gemmatimonas, were enriched in the soil when SDZ was present while the abundance of bacteria which typically contribute to high soil quality belonging to the genera Pseudomonas and Lysobacter, Hydrogenophaga, and Adhaeribacter decreased in response to the repeated application of manure and SDZ.
Dynamics of Bacterial Communities during the Ripening Process of Different Croatian Cheese Types Derived from Raw Ewe's Milk Cheeses
Mirna Mrkonji? Fuka, Stefanie Wallisch, Marion Engel, Gerhard Welzl, Jasmina Havranek, Michael Schloter
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0080734
Abstract: Microbial communities play an important role in cheese ripening and determine the flavor and taste of different cheese types to a large extent. However, under adverse conditions human pathogens may colonize cheese samples during ripening and may thus cause severe outbreaks of diarrhoea and other diseases. Therefore in the present study we investigated the bacterial community structure of three raw ewe's milk cheese types, which are produced without the application of starter cultures during ripening from two production sites based on fingerprinting in combination with next generation sequencing of 16S rRNA gene amplicons. Overall a surprisingly high diversity was found in the analyzed samples and overall up to 213 OTU97 could be assigned. 20 of the major OTUs were present in all samples and include mostly lactic acid bacteria (LAB), mainly Lactococcus, and Enterococcus species. Abundance and diversity of these genera differed to a large extent between the 3 investigated cheese types and in response to the ripening process. Also a large number of non LAB genera could be identified based on phylogenetic alignments including mainly Enterobacteriaceae and Staphylococcacae. Some species belonging to these two families could be clearly assigned to species which are known as potential human pathogens like Staphylococcus saprophyticus or Salmonella spp. However, during cheese ripening their abundance was reduced. The bacterial genera, namely Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Brevibacterium, Corynebacterium, Clostridium, Staphylococcus, Thermoanerobacterium, E. coli, Hafnia, Pseudomonas, Janthinobacterium, Petrotoga, Kosmotoga, Megasphaera, Macrococcus, Mannheimia, Aerococcus, Vagococcus, Weissella and Pediococcus were identified at a relative low level and only in selected samples. Overall the microbial composition of the used milk and the management of the production units determined the bacterial community composition for all cheese types to a large extend, also at the late time points of cheese ripening.
Response of the Abundance of Key Soil Microbial Nitrogen-Cycling Genes to Multi-Factorial Global Changes
Ximei Zhang, Wei Liu, Michael Schloter, Guangming Zhang, Quansheng Chen, Jianhui Huang, Linghao Li, James J. Elser, Xingguo Han
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0076500
Abstract: Multiple co-occurring environmental changes are affecting soil nitrogen cycling processes, which are mainly mediated by microbes. While it is likely that various nitrogen-cycling functional groups will respond differently to such environmental changes, very little is known about their relative responsiveness. Here we conducted four long-term experiments in a steppe ecosystem by removing plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and manipulating some of their combinations. We quantified the abundance of seven nitrogen-cycling genes, including those for fixation (nifH), mineralization (chiA), nitrification (amoA of ammonia-oxidizing bacteria (AOB) or archaea (AOA)), and denitrification (nirS, nirK and nosZ). First, for each gene, we compared its sensitivities to different environmental changes and found that the abundances of various genes were sensitive to distinct and different factors. Overall, the abundances of nearly all genes were sensitive to nitrogen enrichment. In addition, the abundances of the chiA and nosZ genes were sensitive to plant functional group removal, the AOB-amoA gene abundance to phosphorus enrichment when nitrogen was added simultaneously, and the nirS and nirK gene abundances responded to watering. Second, for each single- or multi-factorial environmental change, we compared the sensitivities of the abundances of different genes and found that different environmental changes primarily affected different gene abundances. Overall, AOB-amoA gene abundance was most responsive, followed by the two denitrifying genes nosZ and nirS, while the other genes were less sensitive. These results provide, for the first time, systematic insights into how the abundance of each type of nitrogen-cycling gene and the equilibrium state of all these nitrogen-cycling gene abundances would shift under each single- or multi-factorial global change.
Influence of Different Forest System Management Practices on Leaf Litter Decomposition Rates, Nutrient Dynamics and the Activity of Ligninolytic Enzymes: A Case Study from Central European Forests
Witoon Purahong, Danuta Kapturska, Marek J. Pecyna, Elke Schulz, Michael Schloter, Fran?ois Buscot, Martin Hofrichter, Dirk Krüger
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0093700
Abstract: Leaf litter decomposition is the key ecological process that determines the sustainability of managed forest ecosystems, however very few studies hitherto have investigated this process with respect to silvicultural management practices. The aims of the present study were to investigate the effects of forest management practices on leaf litter decomposition rates, nutrient dynamics (C, N, Mg, K, Ca, P) and the activity of ligninolytic enzymes. We approached these questions using a 473 day long litterbag experiment. We found that age-class beech and spruce forests (high forest management intensity) had significantly higher decomposition rates and nutrient release (most nutrients) than unmanaged deciduous forest reserves (P<0.05). The site with near-to-nature forest management (low forest management intensity) exhibited no significant differences in litter decomposition rate, C release, lignin decomposition, and C/N, lignin/N and ligninolytic enzyme patterns compared to the unmanaged deciduous forest reserves, but most nutrient dynamics examined in this study were significantly faster under such near-to-nature forest management practices. Analyzing the activities of ligninolytic enzymes provided evidence that different forest system management practices affect litter decomposition by changing microbial enzyme activities, at least over the investigated time frame of 473 days (laccase, P<0.0001; manganese peroxidase (MnP), P = 0.0260). Our results also indicate that lignin decomposition is the rate limiting step in leaf litter decomposition and that MnP is one of the key oxidative enzymes of litter degradation. We demonstrate here that forest system management practices can significantly affect important ecological processes and services such as decomposition and nutrient cycling.
Different Land Use Intensities in Grassland Ecosystems Drive Ecology of Microbial Communities Involved in Nitrogen Turnover in Soil
Annabel Meyer, Andreas Focks, Viviane Radl, Daniel Keil, Gerhard Welzl, Ingo Sch?ning, Steffen Boch, Sven Marhan, Ellen Kandeler, Michael Schloter
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0073536
Abstract: Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity.
Soil Environmental Conditions and Microbial Build-Up Mediate the Effect of Plant Diversity on Soil Nitrifying and Denitrifying Enzyme Activities in Temperate Grasslands
Xavier Le Roux, Bernhard Schmid, Franck Poly, Romain L. Barnard, Pascal A. Niklaus, Nadine Guillaumaud, Maike Habekost, Yvonne Oelmann, Laurent Philippot, Joana Falcao Salles, Michael Schloter, Sibylle Steinbeiss, Alexandra Weigelt
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061069
Abstract: Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number – namely richness, presence of particular plant functional groups, or particular combinations of these) and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), the abundance of nitrifiers (bacterial and archaeal amoA gene number) and denitrifiers (nirK, nirS and nosZ gene number), and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species), though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification, whereas changes in microbial abundance play a major role for non-facultative activities such as nitrification.
Intra-versus inter-site macroscale variation in biogeochemical properties along a paddy soil chronosequence
C. Mueller-Niggemann,A. Bannert,M. Schloter,E. Lehndorff
Biogeosciences Discussions , 2011, DOI: 10.5194/bgd-8-10119-2011
Abstract: In order to assess the intrinsic heterogeneity of paddy soils, a set of biogeochemical soil parameters was investigated in five field replicates of seven paddy fields (50, 100, 300, 500, 700, 1000, and 2000 yr of wetland rice cultivation), one flooded paddy nursery, one tidal wetland (TW), and one freshwater site (FW) from a coastal area at Hangzhou Bay, Zhejiang Province, China. All soils evolved from a marine tidal flat substrate due to land reclamation. The biogeochemical parameters based on their properties were differentiated into (i) a group behaving conservatively (TC, TOC, TN, TS, magnetic susceptibility, soil lightness and colour parameters, δ13C, δ15N, lipids and n-alkanes) and (ii) one encompassing more labile properties or fast cycling components (Nmic, Cmic, nitrate, ammonium, DON and DOC). The macroscale heterogeneity in paddy soils was assessed by evaluating intra- versus inter-site spatial variability of biogeochemical properties using statistical data analysis (descriptive, explorative and non-parametric). Results show that the intrinsic heterogeneity of paddy soil organic and minerogenic components per field is smaller than between study sites. The coefficient of variation (CV) values of conservative parameters varied in a low range (10 % to 20 %), decreasing from younger towards older paddy soils. This indicates a declining variability of soil biogeochemical properties in longer used cropping sites according to progress in soil evolution. A generally higher variation of CV values (>20–40 %) observed for labile parameters implies a need for substantially higher sampling frequency when investigating these as compared to more conservative parameters. Since the representativeness of the sampling strategy could be sufficiently demonstrated, an investigation of long-term carbon accumulation/sequestration trends in topsoils of the 2000 year paddy chronosequence under wetland rice cultivation was conducted. The evolutionary trend showed that the biogeochemical signatures characteristic for paddy soils were fully developed in less than 300 yr since onset of wetland rice cultivation. A six-fold increase of topsoil TOC suggests a substantial gain in CO2 sequestration potential when marine tidal wetland substrate developed to 2000 year old paddy soil.
Intra- versus inter-site macroscale variation in biogeochemical properties along a paddy soil chronosequence
C. Mueller-Niggemann,A. Bannert,M. Schloter,E. Lehndorff
Biogeosciences (BG) & Discussions (BGD) , 2012, DOI: 10.5194/bg-9-1237-2012
Abstract: In order to assess the intrinsic heterogeneity of paddy soils, a set of biogeochemical soil parameters was investigated in five field replicates of seven paddy fields (50, 100, 300, 500, 700, 1000, and 2000 yr of wetland rice cultivation), one flooded paddy nursery, one tidal wetland (TW), and one freshwater site (FW) from a coastal area at Hangzhou Bay, Zhejiang Province, China. All soils evolved from a marine tidal flat substrate due to land reclamation. The biogeochemical parameters based on their properties were differentiated into (i) a group behaving conservatively (TC, TOC, TN, TS, magnetic susceptibility, soil lightness and colour parameters, δ13C, δ15N, lipids and n-alkanes) and (ii) one encompassing more labile properties or fast cycling components (Nmic, Cmic, nitrate, ammonium, DON and DOC). The macroscale heterogeneity in paddy soils was assessed by evaluating intra- versus inter-site spatial variability of biogeochemical properties using statistical data analysis (descriptive, explorative and non-parametric). Results show that the intrinsic heterogeneity of paddy soil organic and minerogenic components per field is smaller than between study sites. The coefficient of variation (CV) values of conservative parameters varied in a low range (10% to 20%), decreasing from younger towards older paddy soils. This indicates a declining variability of soil biogeochemical properties in longer used cropping sites according to progress in soil evolution. A generally higher variation of CV values (>20–40%) observed for labile parameters implies a need for substantially higher sampling frequency when investigating these as compared to more conservative parameters. Since the representativeness of the sampling strategy could be sufficiently demonstrated, an investigation of long-term carbon accumulation/sequestration trends in topsoils of the 2000 yr paddy chronosequence under wetland rice cultivation restricted was conducted. Observations cannot be extrapolated to global scale but with coastal paddy fields developed on marine tidal flat substrates after land reclamation in the Zhejiang Province represent a small fraction (<1%) of the total rice cropping area. The evolutionary trend showed that the biogeochemical signatures characteristic for paddy soils were fully developed in less than 300 yr since onset of wetland rice cultivation. A six-fold increase of topsoil TOC suggests a substantial gain in CO2 sequestration potential when marine tidal wetland substrate developed to 2000 yr old paddy soil.
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