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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: Biophysical Journal, 04 March 2014, Vol.106(5), pp.1079-1091
    Description: Membrane pearling in live cells is observed when the plasma membrane is depleted of its support, the cortical actin network. Upon efficient depolymerization of actin, pearls of variable size are formed, which are connected by nanotubes of ∼40 nm diameter. We show that formation of the membrane tubes and their transition into chains of pearls do not require external tension, and that they neither depend on microtubule-based molecular motors nor pressure generated by myosin-II. Pearling thus differs from blebbing. The pearling state is stable as long as actin is prevented from polymerizing. When polymerization is restored, the pearls are retracted into the cell, indicating continuity of the membrane. Our data suggest that the alternation of pearls and strings is an energetically favored state of the unsupported plasma membrane, and that one of the functions of the actin cortex is to prevent the membrane from spontaneously assuming this configuration.
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
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  • 3
    Language: English
    In: PLoS ONE, 2012, Vol.7(7), p.e40467
    Description: The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the introduction of amplicon pyrosequencing. The possibility of barcoding gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing, similar to the early days of community fingerprinting. In this study we demonstrate the reproducibility of bacterial 454 pyrotag sequencing over biological and technical replicates of aquifer sediment bacterial communities. Moreover, we explore the potential of recovering specific template ratios via quantitatively defined template spiking to environmental DNA. We sequenced pyrotag libraries of triplicate sediment samples taken in annual sampling campaigns at a tar oil contaminated aquifer in Düsseldorf, Germany. The abundance of dominating lineages was highly reproducible with a maximal standard deviation of ∼4% read abundance across biological, and ∼2% across technical replicates. Our workflow also allows for the linking of read abundances within defined assembled pyrotag contigs to that of specific ‘ in vivo ’ fingerprinting signatures. Thus we demonstrate that both terminal restriction fragment length polymorphism (T-RFLP) analysis and pyrotag sequencing are capable of recovering highly comparable community structure. Overall diversity was roughly double in amplicon sequencing. Pyrotag libraries were also capable of linearly recovering increasing ratios (up to 20%) of 16S rRNA gene amendments from a pure culture of Aliivibrio fisheri spiked to sediment DNA. Our study demonstrates that 454 pyrotag sequencing is a robust and reproducible method, capable of reliably recovering template abundances and overall community structure within natural microbial communities.
    Keywords: Research Article ; Biology ; Microbiology ; Ecology ; Marine And Aquatic Sciences
    E-ISSN: 1932-6203
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  • 4
    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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  • 5
    Language: English
    Description: BACKGROUND: Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited. METHODS: Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons. RESULTS: We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype. CONCLUSION: Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system.
    Keywords: Chronic obstructive pulmonary disease ; Ribosomal rna ; Microbiome ; Emphysema ; Prevotella ; Fusobacteria ; Computed axial tomography ; Streptococcus
    ISSN: 1932-6203
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  • 6
    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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  • 7
    Language: English
    In: Plant and Soil, 2016, Vol.407(1), pp.203-215
    Description: Background and aims Forest ecosystems may act as sinks for or source of atmospheric CO.sub.2. While inorganic nitrogen (N) fertilization increases aboveground tree biomass, the effects on soil and rhizosphere microorganisms are less clear, indicating potentially unpredictable changes in nutrient cycling processes maintaining ecosystem functioning. Although plant-derived carbon (C) is the main C source in soils during the vegetation period, information on the response of rhizosphere bacteria assimilating rhizodeposits to increased soil N availability mainly for trees is missing. Methods We performed a greenhouse experiment with .sup.13C-CO.sub.2 labelled young beech seedlings grown under different N fertilization levels. DNA Stable Isotope Probing (DNA-SIP) in combination with TRFLP and pyrosequencing enabled us to identify bacteria assimilating plant-derived C and to assess the main responders phylogenetically. Results Although above- and belowground allocation of recently fixed photosynthates remained unchanged, microbial rhizosphere community composition was clearly affected by fertilization. Besides, we found lower .sup.13C incorporation into microbial biomass in fertilized soil. Moreover, it could be shown that only a small subset of the rhizosphere microbiome incorporated recently fixed C into its DNA, dominated by Proteobacteria (Alpha- and Betaproteobacteria) and Actinobacteria (Actinomycetales). Conclusions Our results suggest that N fertilization may change both the diversity of bacterial communities using rhizodeposits and assimilation rates of recently fixed photosynthates. Given the close interaction of beneficial and/or deleterious microbes and plants in the rhizosphere, this could potentially have positive or negative implications for plant performance on long-term.
    Keywords: Fertilization ; Plant-derived carbon ; Rhizosphere microbiome ; DNA-SIP ; Pyrosequencing
    ISSN: 0032-079X
    E-ISSN: 1573-5036
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  • 8
    Language: English
    In: PLoS ONE, 01 January 2013, Vol.8(11), p.e80734
    Description: 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.
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 9
    Language: English
    In: Microbial Ecology, 2011, Vol.62(4), pp.959-972
    Description: Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n -alkanes with a chain length between C 5 and C 16 at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n -alkane-degrading bacteria was quantified via real-time PCR of alkB , whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n -alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones ( Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of hydrocarbon-degrading bacteria to the contamination at the molecular level.
    Keywords: Enzymes -- Physiological Aspects ; Enzymes -- Analysis ; Metal Industries -- Physiological Aspects ; Metal Industries -- Analysis ; Soil Ecology -- Physiological Aspects ; Soil Ecology -- Analysis ; Genetic Research -- Physiological Aspects ; Genetic Research -- Analysis ; Biodiversity -- Physiological Aspects ; Biodiversity -- Analysis ; Biodegradation -- Physiological Aspects ; Biodegradation -- Analysis ; Forest Soils -- Physiological Aspects ; Forest Soils -- Analysis ; Genes -- Physiological Aspects ; Genes -- Analysis ; Soil Microbiology -- Physiological Aspects ; Soil Microbiology -- Analysis;
    ISSN: 0095-3628
    E-ISSN: 1432-184X
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  • 10
    Language: English
    In: Journal of Microbiological Methods, July 2013, Vol.94(1), pp.30-36
    Description: The plant root interface is a hot spot for microbial activities. Root exudates are the key compounds that drive microbial performance. However quality and amount of root exudates are highly dynamic in time and space, thus a direct influence of a single compound on a microbial community composition is fairly impossible to study in nature. Therefore it was the aim of this project to develop an artificial root model (ARM), and investigate the influence of three compounds which have often been described as root exudates acting as model compounds for carbohydrates, organic acids and amino acids (glucose, malic acid and serine) on the development of bacterial communities and time on the ARM based on 16S rRNA derived TRFLP pattern. The ARM consisted of a slide covered with low melting agarose, where 8 different compounds which have been described as typical root exudates were embedded. The ARMs were incubated in soil for 2, 5, 9 and 20 days, before the analysis of the developed bacterial community structure was done. The bacterial community composition was in good agreement after 9 days of incubation of the ARM in soil with the root associated microflora of shortly before flowering. The single compounds of the exudates mix had different effects on the development of ARM derived bacterial communities. Whereas the experiments where glucose was omitted gave no significant differences in the development of bacterial communities over time compared to the ARM where the standard mixture of exudates had been applied, there was a pronounced effect visible mainly after two days of incubation of the ARM in the experiments where no malic acid was added to the exudate mixture. At later time points ARMs with standard exudates' mixture and those where malic acid had been omitted, the bacterial community composition did not differ. The experiments where serine was omitted mainly induced shifts in the bacterial community composition compared to the ARM with standard exudates' mixture at the latest sampling time point (20 days of incubation).
    Keywords: Roots ; Bacterial Communities ; 16s Rrna Fingerprinting ; Exudates ; A. Thaliana ; Biology
    ISSN: 0167-7012
    E-ISSN: 1872-8359
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