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  • 1
    Language: English
    In: PLoS ONE, Jan 5, 2016, Vol.11(1)
    Description: The quality and safety of raw milk still remains a worldwide challenge. Culture-dependent methods indicated that the continuous N.sub.2 gas-flushing of raw milk reduced the bacterial growth during cold storage by up to four orders of magnitude, compared to cold storage alone. This study investigated the influence of N.sub.2 gas-flushing on bacterial diversity in bovine raw-milk samples, that were either cold stored at 6#176;C or additionally flushed with pure N.sub.2 for up to one week. Next-generation sequencing (NGS) of the V1-V2 hypervariable regions of 16S rRNA genes, derived from amplified cDNA, which was obtained from RNA directly isolated from raw-milk samples, was performed. The reads, which were clustered into 2448 operational taxonomic units (OTUs), were phylogenetically classified. Our data revealed a drastic reduction in the diversity of OTUs in raw milk during cold storage at 6#176;C at 97% similarity level; but, the N.sub.2 -flushing treatment alleviated this reduction and substantially limited the loss of bacterial diversity during the same cold-storage period. Compared to cold-stored milk, the initial raw-milk samples contained less Proteobacteria (mainly Pseudomonadaceae, Moraxellaceae and Enterobacteriaceae) but more Firmicutes (mainly Ruminococcaceaea, Lachnospiraceae and Oscillospiraceaea) and Bacteroidetes (mainly Bacteroidales). Significant differences between cold-stored and additionally N.sub.2 -flushed milk were mainly related to higher levels of Pseudomononadaceae (including the genera Pseudomonas and Acinetobacter) in cold-stored milk samples; furthermore, rare taxa were better preserved by the N.sub.2 gas flushing compared to the cold storage alone. No major changes in bacterial composition with time were found regarding the distribution of the major 9 OTUs, that dominated the Pseudomonas genus in N.sub.2 -flushed or non-flushed milk samples, other than an intriguing predominance of bacteria related to P. veronii. Overall, this study established that neither bacteria causing milk spoilage nor any well-known human pathogen or anaerobe benefited from the N.sub.2 gas flushing even though the N.sub.2 -flushed and non-flushed cold-stored milk differed in bacterial counts by up to 10.sup.4 -fold.
    Keywords: Milk -- Quality Management ; Pseudomonas -- Research
    ISSN: 1932-6203
    Source: Cengage Learning, Inc.
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  • 2
    Language: English
    In: PLoS ONE, 01 January 2016, Vol.11(1), p.e0146015
    Description: The quality and safety of raw milk still remains a worldwide challenge. Culture-dependent methods indicated that the continuous N2 gas-flushing of raw milk reduced the bacterial growth during cold storage by up to four orders of magnitude, compared to cold storage alone. This study investigated...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: Chemosphere, June 2011, Vol.84(1), pp.182-186
    Description: ► We compared the effect of DMPP on ammonia-oxidizing bacteria and archaea. ► DMPP only affected the bacteria, whereas the archaea remained unaffected. ► This effect was observed in both, rhizosphere and bulk soil. In agricultural plant production nitrification inhibitors like 3,4-dimethylpyrazole phosphate (DMPP) are used to retard the microbial nitrification process of fertilized ammonium to enhance the nitrogen supply for cultivated crops and to reduce nitrogen losses from the production system. Besides the well-known ammonia-oxidizing bacteria (AOB) it is known for a few years that also ammonia-oxidizing archaea (AOA) are able to perform the first step in nitrification, hence being also a target for a nitrification inhibitor. However, so far no information are available concerning the effectiveness of DMPP and its extent towards AOB and AOA, neither in bulk soil nor in the root-rhizosphere complex. We investigated in a field experiment performed according to agricultural practice the effect of DMPP on the abundance of AOB and AOA two, four and eight weeks after fertilization. We observed impaired abundances of AOB but not of AOA in both soil compartments that were still visible eight weeks after application, possibly indicating a reduced effectiveness of the nitrification inhibitor in our study.
    Keywords: Nitrification Inhibitor ; Dmpp ; Ammonia-Oxidizing Bacteria ; Ammonia-Oxidizing Archaea ; Quantitative Real-Time Pcr ; Arable Soil ; Chemistry ; Ecology
    ISSN: 0045-6535
    E-ISSN: 1879-1298
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  • 4
    Language: English
    In: PLoS ONE, 2017, Vol.12(12)
    Description: We explored the assembly of intestinal microbiota in healthy male participants during the randomized crossover design of run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bed rest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, with balanced...
    Keywords: Medical And Health Sciences ; Basic Medicine ; Microbiology In The Medical Area ; Medicin Och Hälsovetenskap ; Medicinska Och Farmaceutiska Grundvetenskaper ; Mikrobiologi Inom Det Medicinska Området
    ISSN: 1932-6203
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  • 5
    In: Scientific Reports, 2017, Vol.7
    Description: Sand dunes are unique ecosystems with distinct features which limited the accumulation of biomass. The distance from seashore affects both the physical properties of the sand dunes and the biota living above- and below ground. The goal of the present study was to determine the effects of the distance from shore to inland on soil bacterial community composition during wet and dry season. We studied a chronosequence of sites close to the eastern Mediterranean coast. Bacterial diversity was assessed using directly extracted DNA from soil samples and 16 S ribosomal RNA gene fingerprinting. Our data indicates a significant influence of season and site on bacterial community structure. We showed that during the wet season soil organic matter, pH and salinity strongly influence bacterial community composition, whereas during the dry period bacterial diversity was mainly driven by the shortage of water at all sites. Consequently diversity was lowest during dry season at dunes close to the shore, whereas during the wet season the higher water content and the reduced salinity at the dunes which are more at the inland induced an increase in diversity, which illustrates the pronounced dynamics of microbial communities in soil over a season mainly at inland dunes.
    Keywords: Rrna ; DNA Fingerprinting ; Community Structure ; Biomass ; Salinity Effects ; Community Composition ; Sand ; Soil Microorganisms ; Dunes ; Salinity ; Water Content ; Organic Matter ; Ph Effects ; Deoxyribonucleic Acid–DNA ; Organic Soils;
    E-ISSN: 2045-2322
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  • 6
    In: Microbial Biotechnology, July 2016, Vol.9(4), pp.502-513
    Description: Cyanides are highly toxic and produced by various microorganisms as defence strategy or to increase their competitiveness. As degradation is the most efficient way of detoxification, some microbes developed the capability to use cyanides as carbon and nitrogen source. However, it is not clear if this potential also helps to lower cyanide concentrations in roadside soils where deicing salt application leads to significant inputs of ferrocyanide. The question remains if biodegradation in soils can occur without previous photolysis. By conducting a microcosm experiment using soils with/without pre‐exposition to road salts spiked with C‐labelled ferrocyanide, we were able to confirm biodegradation and in parallel to identify bacteria using ferrocyanide as C source via stable isotope probing ), fingerprinting and pyrosequencing. Bacteria assimilating C were highly similar in the pre‐exposed soils, belonging mostly to (,,). In the soil without pre‐exposition, bacteria belonging to Aci (Gp3, Gp4, Gp6), () and (,) used ferrocyanide as C source but not the present . This indicated that (i) various bacteria are able to assimilate ferrocyanide‐derived C and (ii) long‐term exposition to ferrocyanide applied with deicing salts leads to outcompeting other microorganisms for the use of ferrocyanide as C source. Deicing salt application leads to significant inputs of ferrocyanide into the road environment, having the potential to release highly toxic cyanide compounds. Despite its ecological relevance, data on its fate are missing so far. Our results revealed (1) that biodegradation in soil occured and (2) that bacteria using ferrocyanide as carbon source were highly similar in pre‐exposed soils, belonging mostly to , whereas in soils without pre‐exposition bacteria belonging to but not the present assimilated ferrocyanide‐derived carbon.
    Keywords: Cyanides ; Photolysis ; Biodegradation ; Bacteria ; Nucleic Acids ; Phylogeny ; Soil Carbon ; Iron Compounds;
    ISSN: 1751-7915
    E-ISSN: 1751-7915
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  • 7
    Language: English
    In: Microbial Ecology, 2015, Vol.69(4), pp.867-878
    Description: Soil microbial community responses to elevated atmospheric CO 2 concentrations (eCO 2 ) occur mainly indirectly via CO 2 -induced plant growth stimulation leading to quantitative as well as qualitative changes in rhizodeposition and plant litter. In order to gain insight into short-term, site-specific effects of eCO 2 on the microbial community structure at the plant-soil interface, young beech trees ( Fagus sylvatica L.) from two opposing mountainous slopes with contrasting climatic conditions were incubated under ambient (360 ppm) CO 2 concentrations in a greenhouse. One week before harvest, half of the trees were incubated for 2 days under eCO 2 (1,100 ppm) conditions. Shifts in the microbial community structure in the adhering soil as well as in the root rhizosphere complex (RRC) were investigated via TRFLP and 454 pyrosequencing based on 16S ribosomal RNA (rRNA) genes. Multivariate analysis of the community profiles showed clear changes of microbial community structure between plants grown under ambient and elevated CO 2 mainly in RRC. Both TRFLP and 454 pyrosequencing showed a significant decrease in the microbial diversity and evenness as a response of CO 2 enrichment. While Alphaproteobacteria dominated by Rhizobiales decreased at eCO 2 , Betaproteobacteria , mainly Burkholderiales , remained unaffected. In contrast, Gammaproteobacteria and Deltaproteobacteria, predominated by Pseudomonadales and Myxococcales , respectively, increased at eCO 2 . Members of the order Actinomycetales increased, whereas within the phylum Acidobacteria subgroup Gp1 decreased, and the subgroups Gp4 and Gp6 increased under atmospheric CO 2 enrichment. Moreover, Planctomycetes and Firmicutes , mainly members of Bacilli , increased under eCO 2 . Overall, the effect intensity of eCO 2 on soil microbial communities was dependent on the distance to the roots. This effect was consistent for all trees under investigation; a site-specific effect of eCO 2 in response to the origin of the trees was not observed.
    Keywords: Rhizosphere ; Beech ; Bacterial communities ; CO
    ISSN: 0095-3628
    E-ISSN: 1432-184X
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  • 8
    Language: English
    In: Microbial Ecology, 2018, Vol.75(4), pp.830-833
    Description: While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales , Planctomycetales , Rhizobiales , and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere. The latter two, as well as Xanthomonadales , Sphingomonadales , and Caulobacterales showed a significantly higher abundance in pre-dawn samples compared to post-dawn samples. These changes in taxonomy coincide with functional changes as genes involved in both carbohydrate and amino acid metabolism were more abundant in pre-dawn samples compared to post-dawn samples. This study significantly enhances our present knowledge on how rhizospheric microbiota perceives and responds to changes in the soil during dark and light periods.
    Keywords: Rhizosphere ; Metatranscriptome ; Barley ; Diurnal cycle ; Microbial dynamics
    ISSN: 0095-3628
    E-ISSN: 1432-184X
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  • 9
    Language: English
    In: Sci Rep, 2017, Vol.7(1), pp.4205-4205
    Description: Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker. Furthermore, cultivation-based approaches were used to obtain isolates of the major taxa to study their ecophysiology. The endophytic microbiome from P. pinaster trees differed significantly between the two sampling sites. Main bacterial OTUs belonged to the Proteobacteria (39% (site M) - 97% (site A)), and Firmicutes (0.70% (site A) - 44% (site M)). However, consequences of the invasion with the pathogen were comparable. Interestingly diversity of wood endophytic bacteria increased with the severity of the diseases, with highest diversity levels observed in in the most affected trees. Our results suggest that in the first stages of the disease, the defence mechanisms of plants are repressed by the pathogen, resulting in a colonization of the wood interior by soil microorganisms.
    Keywords: Biology;
    ISSN: 2045-2322
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  • 10
    Language: English
    In: Journal of Microbiological Methods, June 2016, Vol.125, pp.91-97
    Description: Phosphorus (P) is of central importance for cellular life but likewise a limiting macronutrient in numerous environments. Certainly microorganisms have proven their ability to increase the phosphorus bioavailability by mineralization of organic-P and solubilization of inorganic-P. On the other hand they efficiently take up P and compete with other biota for phosphorus. However the actual microbial community that is associated to the turnover of this crucial macronutrient in different ecosystems remains largely anonymous especially taking effects of seasonality and spatial heterogeneity into account. In this study seven oligonucleotide primers are presented which target genes coding for microbial acid and alkaline phosphatases ( , ), phytases ( ), phosphonatases ( ) as well as the quinoprotein glucose dehydrogenase ( ) and different P transporters ( , ). Illumina amplicon sequencing of soil genomic DNA underlined the high rate of primer specificity towards the respective target gene which usually ranged between 98% and 100% ( : 87%). As expected the primers amplified genes from a broad diversity of distinct microorganisms. Using DNA from a beech dominated forest soil, the highest microbial diversity was detected for the alkaline phosphatase ( ) gene which was amplified from 15 distinct phyla respectively 81 families. Noteworthy the primers also allowed amplification of from 6 fungal orders. The genes coding for acid phosphatase ( ) and the quinoprotein glucose dehydrogenase ( ) were amplified from 20 respectively 17 different microbial orders. In comparison the phytase and phosphonatase ( , ) primers covered 13 bacterial orders from 2 different phyla respectively. Although the amplified microbial diversity was apparently limited both primers reliably detected all orders that contributed to the P turnover in the investigated soil as revealed by a previous metagenomic approach. Genes that code for microbial P transporter ( , ) were amplified from 13 respectively 9 distinct microbial orders. Accordingly the introduced primers represent a valuable tool for further analysis of the microbial community involved in the turnover of phosphorus in soils but most likely also in other environments.
    Keywords: Phosphorus Turnover ; Forest Soil ; Phod ; Phon ; Appa ; Pita ; Psts ; Biology
    ISSN: 0167-7012
    E-ISSN: 1872-8359
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