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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 17 May 2011, Vol.108(20), pp.8420-5
    Description: Genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (AOA) might play a major role in nitrification on Earth. However, only one pure isolate of this group from a marine environment has so far been obtained, demonstrating archaeal ammonia oxidation coupled with autotrophic growth similar to the bacterial counterparts. Here we describe the cultivation and isolation of an AOA from soil. It grows on ammonia or urea as an energy source and is capable of using higher ammonia concentrations than the marine isolate, Nitrosopumilus maritimus. Surprisingly, although it is able to grow chemolithoautotrophically, considerable growth rates of this strain are obtained only upon addition of low amounts of pyruvate or when grown in coculture with bacteria. Our findings expand the recognized metabolic spectrum of AOA and help explain controversial results obtained in the past on the activity and carbon assimilation of these globally distributed organisms.
    Keywords: Soil Microbiology ; Ammonia -- Metabolism ; Archaea -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: PloS one, 2014, Vol.9(12), pp.e114278
    Description: Ongoing climate change will lead to more extreme weather events, including severe drought periods and intense drying rewetting cycles. This will directly influence microbial nitrogen (N) turnover rates in soil by changing the water content and the oxygen partial pressure. Therefore, a space for time climate change experiment was conducted by transferring intact beech seedling-soil mesocosms from a northwest (NW) exposed site, representing today's climatic conditions, to a southwest (SW) exposed site, providing a model climate for future conditions with naturally occurring increased soil temperature (+0.8°C in average). In addition, severe drought and intense rainfall was simulated by a rainout shelter at SW and manual rewetting after 39 days drought, respectively. Soil samples were taken in June, at the end of the drought period (August), 24 and 72 hours after rewetting (August) and after a regeneration period of four weeks (September). To follow dynamics of bacterial and archaeal communities involved in N turnover, abundance and activity of nitrifiers, denitrifiers, N2-fixing microbes and N-mineralizers was analyzed based on marker genes and the related transcripts by qPCR from DNA and RNA directly extracted from soil. Abundance of the transcripts was reduced under climate change with most pronounced effects for denitrification. Our results revealed that already a transfer from NW to SW without further treatment resulted in decreased cnor and nosZ transcripts, encoding for nitric oxide reductase and nitrous oxide reductase, respectively, while nirK transcripts, encoding for nitrite reductase, remained unaffected. Severe drought additionally led to reduced nirK and cnor transcripts at SW. After rewetting, nirK transcripts increased rapidly at both sites, while cnor and nosZ transcripts increased only at NW. Our data indicate that the climate change influences activity pattern of microbial communities involved in denitrification processes to a different extend, which may impact emission rates of the greenhouse gas N2O.
    Keywords: Climate Change ; Soil ; Archaea -- Metabolism ; Bacteria -- Metabolism ; Fagus -- Metabolism ; Nitrogen -- Metabolism
    E-ISSN: 1932-6203
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  • 3
    In: PLoS ONE, 2015, Vol.10(8)
    Description: Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.
    Keywords: Research Article
    E-ISSN: 1932-6203
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  • 4
    In: PLoS ONE, 2015, Vol.10(3)
    Description: Due to the high diversity of bacteria in many ecosystems, their slow generation times, specific but mostly unknown nutrient requirements and syntrophic interactions, isolation based approaches in microbial ecology mostly fail to describe microbial community structure. Thus, cultivation independent techniques, which rely on directly extracted nucleic acids from the environment, are a well-used alternative. For example, bacterial automated ribosomal intergenic spacer analysis (B-ARISA) is one of the widely used methods for fingerprinting bacterial communities after PCR-based amplification of selected regions of the operon coding for rRNA genes using community DNA. However, B-ARISA alone does not provide any taxonomic information and the results may be severely biased in relation to the primer set selection. Furthermore, amplified DNA stemming from mitochondrial or chloroplast templates might strongly bias the obtained fingerprints. In this study, we determined the applicability of three different B-ARISA primer sets to the study of bacterial communities. The results from in silico analysis harnessing publicly available sequence databases showed that all three primer sets tested are specific to bacteria but only two primers sets assure high bacterial taxa coverage (1406f/23Sr and ITSF/ITSReub). Considering the study of bacteria in a plant interface, the primer set ITSF/ITSReub was found to amplify ( in silico ) sequences of some important crop species such as Sorghum bicolor and Zea mays . Bacterial genera and plant species potentially amplified by different primer sets are given. These data were confirmed when DNA extracted from soil and plant samples were analyzed. The presented information could be useful when interpreting existing B-ARISA results and planning B-ARISA experiments, especially when plant DNA can be expected.
    Keywords: Research Article
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: Soil Biology and Biochemistry, August, 2014, Vol.75, p.197(5)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2014.04.018 Byline: Marie Uksa, Doreen Fischer, Gerhard Welzl, Timo Kautz, Ulrich Kopke, Michael Schloter Abstract: Spatial and temporal dynamics of microbial community structure and function in subsoils have been rarely studied in the past. In this paper we present data on how bacterial communities as well as selected functional groups of microbes change in the rhizosphere, the drilosphere, and in bulk soil over time in topsoil as well as in subsoil. We show that the overall richness of bacteria and abundance of nitrifiers and denitrifiers decreases in bulk soil with soil depth. However, these effects were not or to a much lower degree observed in the rhizosphere and the drilosphere. Temporal fluctuations contributed by far less than spatial factors to the dynamics of bacterial communities and abundance of nitrifiers and denitrifiers in all compartments independent from the soil depth. Author Affiliation: (a) Helmholtz Zentrum Munchen, Research Unit Environmental Genomics, Ingolstadter Landstr. 1, 85758 Oberschleissheim, Germany (b) University of Bonn, Institute of Organic Agriculture, Katzenburgweg 3, 53115 Bonn, Germany Article History: Received 13 November 2013; Revised 8 April 2014; Accepted 11 April 2014
    Keywords: Genetic Research
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 6
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 27 December 2011, Vol.108(52), pp.21206-11
    Description: Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH 〈5), acido-neutral (5 ≤ pH 〈7), or alkalinophilic (pH ≥ 7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5-8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5-7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.
    Keywords: Soil Microbiology ; Adaptation, Biological -- Genetics ; Ammonia -- Metabolism ; Archaea -- Genetics ; Oxidoreductases -- Genetics ; Soil -- Chemistry
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 7
    Language: English
    In: Applied and Environmental Microbiology, Sept 1, 2015, Vol.81(17), pp.5957-5967
    Description: Study is conducted to test the hypothesis that ectomycorrhizal communities and the free-living rhizosphere microbes from beech trees from sites with two distinct climatic conditions shows differences in N acquisition. To test these hypotheses, young trees from dryer conditions and also from cooler, moist climate conditions are transplanted and it concluded that the ectomycorrhizal community influences N transfer to its host and fungal community from dry condition are efficient in N acquisition.
    Keywords: Mycorrhizae – Research ; Mycorrhizae – Physiological Aspects ; Beeches – Research ; Beeches – Physiological Aspects
    ISSN: 0099-2240
    Source: Cengage Learning, Inc.
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  • 8
    Language: English
    In: Soil Biology and Biochemistry, 2015, Vol.89, p.44(8)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2015.06.018 Byline: Marie Spohn, Nicole Simone Treichel, Michael Cormann, Michael Schloter, Doreen Fischer Abstract: Despite the importance of the rhizosphere for nutrient turnover, little is known about the spatial patterns of organic phosphorus mineralization by plants and by microorganisms in the rhizosphere. Therefore, the distribution of acid and alkaline phosphatase activity and the abundance of bacteria belonging to various bacterial phyla were investigated in the rhizosphere of barley (Hordeum vulgare L.) as dependent on the availability of inorganic P. For this purpose, we conducted a greenhouse experiment with barley growing in inclined boxes that can be opened to the bottom side (rhizoboxes), and applied soil zymography and fluorescence-in situ-hybridization (FISH). Acid phosphatase activity was strongly associated with the root and was highest at the root tips. Due to P fertilization, acid phosphatase activity decreased in the bulk soil, and less strongly in the rhizosphere. Alkaline phosphatase activity, i.e., microbial phosphatase activity was high throughout the soil in the control treatment and was reduced due to inorganic P fertilization especially in the rhizosphere and less strongly in the bulk soil. P-fertilization slightly increased the total number of bacteria in the rhizosphere. Moreover, P-fertilization decreased the abundance of Firmicutes and increased the abundances of Beta- and Gamma-Proteobacteria. The total number of bacterial cells was significantly higher at the root surface than at the root tip and at a distance of 30 [mu]m from the root surface. Our results show that alkaline phosphatase activity decreased more strongly in the rhizosphere than in the bulk soil due to P fertilization, which might be because of greater C deficiency in the bulk soil compared to the rhizosphere. Furthermore, the results indicate a spatial separation between hotspots of acid phosphatase activity and hotspots of bacteria in the rhizosphere of H. vulgare. Taken together, our study shows that bacteria and phosphatase activity were very heterogeneously distributed in soil, and that the effects of P fertilization on phosphatase activity differed strongly between bulk soil and rhizosphere as well as between various zones of the rhizosphere. Author Affiliation: (a) Department of Soil Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University Bayreuth, Germany (b) Helmholtz Zentrum Munchen, Research Unit Environmental Genomics, Ingolstadter Landstr. 1, 85764 Neuherberg, Germany Article History: Received 9 February 2015; Revised 15 May 2015; Accepted 16 June 2015
    Keywords: Barley ; Soil Ecology ; Phosphatases ; Bacteria
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 9
    Language: English
    In: Plant and soil, 2009, Vol.323(1), pp.1-5
    Description: Includes references ; p. 1-5.
    Keywords: Environmental Management ; Soil Ecology ; Ecosystems ; Resource Allocation;
    ISSN: 0032-079X
    E-ISSN: 15735036
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  • 10
    Language: English
    In: International Journal of Food Microbiology, 2010, Vol.142(1), pp.19-24
    Description: In this work we report on the main bacterial microflora typical for fermentation and ripening of traditional Istrian cheese. Samples from milk as well as Istrian cheese were analyzed during the ripening process by using culture independent molecular fingerprinting methods as well as culture based approaches. Our results indicate changes in bacterial diversity pattern during the ripening process. Differences in bacterial diversity at the same ripening stage among different farms investigated were comparably low. Sequence analysis of the most prominent bands of denaturing gradient gel electrophoresis fingerprints revealed dominance of subs. in all samples and a strong presence of spp. which was also confirmed by plate count analysis.
    Keywords: Istrian Cheese ; 16s Rrna Gene ; Bacterial Diversity ; Lactococcus Lactis Subsp. Lactis ; Biology ; Economics
    ISSN: 0168-1605
    E-ISSN: 1879-3460
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