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MicrobiologyOpen

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https://www.readbyqxmd.com/read/28544612/ecology-adaptation-and-function-of-methane-sulfidic-spring-water-biofilm-microorganisms-including-a-strain-of-anaerobic-fungus-mucor-hiemalis
#1
Enamul Hoque, Johannes Fritscher
Ecological aspects, adaptation, and some functions of a special biofilm and its unique key anaerobic fungus Mucor hiemalis strain EH11 isolated from a pristine spring (Künzing, Bavaria, Germany) are described. The spring's pure nature is characterized by, for example, bubbling methane, marine-salinity, mild hydrothermal (~19.1°C), sulfidic, and reductive-anoxic (Eh : -241 to -253 mV, O2 : ≤ 0.1 mg/L) conditions. It is geoecologically located at the border zone between Bavarian Forest (crystalline rocky mountains) and the moor-like Danube River valley, where geological displacements bring the spring's water from the deeper layers of former marine sources up to the surface...
May 24, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28544594/diversity-of-aromatic-hydroxylating-dioxygenase-genes-in-mangrove-microbiome-and-their-biogeographic-patterns-across-global-sites
#2
Sanderson T P de Sousa, Lucélia Cabral, Gileno Vieira Lacerda Júnior, Valéria M Oliveira
Aromatic hydrocarbons (AH), such as polycyclic aromatic hydrocarbons, are compounds largely found in nature. Aromatic-ring-hydroxylating dioxygenases (ARHD) are proteins involved in AH degradation pathways. We used ARHD functional genes from an oil-impacted mangrove area and compared their diversity with other sites around the world to understand the ARHD biogeographic distribution patterns. For this, a comprehensive database was established with 166 operational protein families (OPFs) from 1,758 gene sequences obtained from 15 different sites worldwide, of which twelve are already published studies and three are unpublished...
May 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28544522/metagenomic-potential-for-and-diversity-of-n-cycle-driving-microorganisms-in-the-bothnian-sea-sediment
#3
Olivia Rasigraf, Julia Schmitt, Mike S M Jetten, Claudia Lüke
The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases...
May 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28523826/occurrence-and-abundance-of-ammonia-oxidizing-archaea-and-bacteria-from-the-surface-to-below-the-water-table-in-deep-soil-and-their-contributions-to-nitrification
#4
Lei Zheng, Xue Zhao, Guibing Zhu, Wei Yang, Chao Xia, Tao Xu
Using molecular biology methods (qualitative and quantitative PCR), we determined the occurrence and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) from a dry inland soil in Basel, Switzerland, and from the riparian zone of Baiyangdian Lake, China. We also determined the contributions of these microorganisms to ammonia oxidization at different depths based on the nitrification rate. The number of archaeal amoA genes (the key functional gene in AOA) was larger than the number of bacterial amoA genes in each sample, suggesting a dominant role for the AOA amoA gene in environments with a low ammonium concentration...
May 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28523739/mechanisms-of-peptide-sex-pheromone-regulation-of-conjugation-in-enterococcus-faecalis
#5
Yuqing Chen, Arpan Bandyopadhyay, Briana K Kozlowicz, Heather A H Haemig, Albert Tai, Wei-Shou Hu, Gary M Dunny
In many gram positive bacteria, horizontal transfer and virulence are regulated by peptide-mediated cell-cell signaling. The heptapeptide cCF10 (C) activates conjugative transfer of the Enterococcus faecalis plasmid pCF10, whereas the iCF10 (I) peptide inhibits transfer. Both peptides bind to the same domain of the master transcription regulator PrgX, a repressor of transcription of the prgQ operon encoding conjugation genes. We show that repression of prgQ by PrgX tetramers requires formation of a pCF10 DNA loop where each of two PrgX DNA-binding sites is occupied by a dimer...
May 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28523731/wble2-transcription-factor-in-streptomyces-griseus-s4-7-plays-an-important-role-in-plant-protection
#6
Hyun Ji Cho, Young Sang Kwon, Da-Ran Kim, Gyeongjun Cho, Seong Won Hong, Dong-Won Bae, Youn-Sig Kwak
Streptomyces griseus S4-7 was originally isolated from the strawberry rhizosphere as a microbial agent responsible for Fusarium wilt suppressive soils. S. griseus S4-7 shows specific and pronounced antifungal activity against Fusarium oxysporum f. sp. fragariae. In the Streptomyces genus, the whi transcription factors are regulators of sporulation, cell differentiation, septation, and secondary metabolites production. wblE2 function as a regulator has emerged as a new group in whi transcription factors. In this study, we reveal the involvement of the wblE2 transcription factor in the plant-protection by S...
May 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28523730/investigating-the-effect-of-carbon-source-on-rabies-virus-glycoprotein-production-in-pichia-pastoris-by-a-transcriptomic-approach
#7
Safa Ben Azoun, Héla Kallel
Several factors affect protein expression in Pichia pastoris, one among them is the carbon source. In this work, we studied the effect of this factor on the expression level of rabies virus glycoprotein (RABV-G) in two recombinant clones harboring seven copies of the gene of interest. The expression was driven either by the constitutive glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter or the inducible alcohol oxidase1 (AOX1) promoter. Clones were compared in terms of cell physiology and carbon source metabolism...
May 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28516483/capabilities-and-limitations-of-dgge-for-the-analysis-of-hydrocarbonoclastic-prokaryotic-communities-directly-in-environmental-samples
#8
Dina M Al-Mailem, Mayada K Kansour, Samir S Radwan
Prokaryotic communities in pristine and oil-contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture-dependent and culture-independent approaches. The former technique was the dilution-plating method. For the latter, total genomic DNA was extracted and the 16S rRNA genes were amplified using a universal bacterial primer pair and primer pairs specific for Actinobacteria, Gammaproteobacteria, and Archaea. The amplicons were resolved using denaturing gradient gel electrophoresis (DGGE) and sequenced, and the sequences were compared to those in GenBank...
May 18, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28503851/characterizing-bacterial-communities-in-paper-production-troublemakers-revealed
#9
Anita Zumsteg, Simon K Urwyler, Joachim Glaubitz
Biofilm formation is a major cause of reduced paper quality and increased down time during paper manufacturing. This study uses Illumina next-generation sequencing to identify the microbial populations causing quality issues due to their presence in biofilms and slimes. The paper defects investigated contained traces of the films and/or slime of mainly two genera, Tepidimonas and Chryseobacterium. The Tepidimonas spp. found contributed on average 68% to the total bacterial population. Both genera have been described previously to be associated with biofilms in paper mills...
May 14, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28488414/a-proteomic-based-investigation-of-potential-copper-responsive-biomarkers-proteins-conceptual-networks-and-metabolic-pathways-featuring-penicillium-janthinellum-from-a%C3%A2-heavy-metal-polluted-ecological-niche
#10
Xin Feng, Jian Xu, Yu Liang, Guo-Li Chen, Xian-Wei Fan, You-Zhi Li
Filamentous fungi-copper (Cu) interactions are very important in the formation of natural ecosystems and the bioremediation of heavy metal pollution. However, important issues at the proteome level remain unclear. We compared six proteomes from Cu-resistant wild-type (WT) Penicillium janthinellum strain GXCR and a Cu-sensitive mutant (EC-6) under 0, 0.5, and 3 mmol/L Cu treatments using iTRAQ. A total of 495 known proteins were identified, and the following conclusions were drawn from the results: Cu tolerance depends on ATP generation and supply, which is relevant to glycolysis pathway activity; oxidative phosphorylation, the TCA cycle, gluconeogenesis, fatty acid synthesis, and metabolism are also affected by Cu; high Cu sensitivity is primarily due to an ATP energy deficit; among ATP generation pathways, Cu-sensitive and Cu-insensitive metabolic steps exist; gluconeogenesis pathway is crucial to the survival of fungi in Cu-containing and sugar-scarce environments; fungi change their proteomes via two routes (from ATP, ATP-dependent RNA helicases (ADRHs), and ribosome biogenesis to proteasomes and from ATP, ADRHs to spliceosomes and/or stress-adapted RNA degradosomes) to cope with changes in Cu concentrations; and unique routes exist through which fungi respond to high environmental Cu...
May 9, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28449380/the-pas-domains-of-the-major-sporulation-kinase-in-bacillus-subtilis-play-a-role-in-tetramer-formation-that-is-essential-for-the%C3%A2-autokinase-activity
#11
Brittany Kiehler, Lindsey Haggett, Masaya Fujita
Sporulation in Bacillus subtilis is induced upon starvation. In a widely accepted model, an N-terminal "sensor" domain of the major sporulation kinase KinA recognizes a hypothetical starvation signal(s) and autophosphorylates a histidine residue to activate the master regulator Spo0A via a multicomponent phosphorelay. However, to date no confirmed signal has been found. Here, we demonstrated that PAS-A, the most N-terminal of the three PAS domains (PAS-ABC), is dispensable for the activity, contrary to a previous report...
April 27, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28436122/metabolic-engineering-of-escherichia-coli-for-production-of-2-phenylethylacetate-from-l-phenylalanine
#12
Daoyi Guo, Lihua Zhang, Hong Pan, Xun Li
In order to meet the need of consumer preferences for natural flavor compounds, microbial synthesis method has become a very attractive alternative to the chemical production. The 2-phenylethanol (2-PE) and its ester 2-phenylethylacetate (2-PEAc) are two extremely important flavor compounds with a rose-like odor. In recent years, Escherichia coli and yeast have been metabolically engineered to produce 2-PE. However, a metabolic engineering approach for 2-PEAc production is rare. Here, we designed and expressed a 2-PEAc biosynthetic pathway in E...
April 24, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28425179/resilience-of-the-prokaryotic-microbial-community-of-acropora-digitifera-to-elevated-temperature
#13
Andrian P Gajigan, Leomir A Diaz, Cecilia Conaco
The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria...
April 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28419759/regulation-of-burkholderia%C3%A2-cenocepacia-biofilm-formation-by-rpon-and-the-c-di-gmp-effector-berb
#14
Mustafa Fazli, Morten Rybtke, Elisabeth Steiner, Elisabeth Weidel, Jens Berthelsen, Julie Groizeleau, Wu Bin, Boo Zhao Zhi, Zhang Yaming, Volkhard Kaever, Michael Givskov, Rolf W Hartmann, Leo Eberl, Tim Tolker-Nielsen
Knowledge about the molecular mechanisms that are involved in the regulation of biofilm formation is essential for the development of biofilm-control measures. It is well established that the nucleotide second messenger cyclic diguanosine monophosphate (c-di-GMP) is a positive regulator of biofilm formation in many bacteria, but more knowledge about c-di-GMP effectors is needed. We provide evidence that c-di-GMP, the alternative sigma factor RpoN (σ54), and the enhancer-binding protein BerB play a role in biofilm formation of Burkholderia cenocepacia by regulating the production of a biofilm-stabilizing exopolysaccharide...
April 16, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28419748/the-known-genetic-potential-for-microbial-communities-to-degrade-organic-phosphorus-is-reduced-in-low-ph-soils
#15
Ian D E A Lidbury, Tandra Fraser, Andrew R J Murphy, David J Scanlan, Gary D Bending, Alexandra M E Jones, Jonathan D Moore, Andrew Goodall, Mark Tibbett, John P Hammond, Elizabeth M H Wellington
In soil, bioavailable inorganic orthophosphate is found at low concentrations and thus limits biological growth. To overcome this phosphorus scarcity, plants and bacteria secrete numerous enzymes, namely acid and alkaline phosphatases, which cleave orthophosphate from various organic phosphorus substrates. Using profile hidden Markov modeling approaches, we investigated the abundance of various non specific phosphatases, both acid and alkaline, in metagenomes retrieved from soils with contrasting pH regimes...
April 16, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28401707/myxobacteria-in-high-moor-and-fen-an-astonishing-diversity-in-a-neglected-extreme-habitat
#16
Kathrin I Mohr, Tanja Zindler, Joachim Wink, Elke Wilharm, Marc Stadler
Increasing antibiotic resistances of numerous pathogens mean that myxobacteria, well known producers of new antibiotics, are becoming more and more interesting. More than 100 secondary metabolites, most of them with bioactivity, were described from the order Myxococcales. Especially new myxobacterial genera and species turned out to be reliable sources for novel antibiotics and can be isolated from uncommon neglected habitats like, for example, acidic soils. Almost nothing is known about the diversity of myxobacteria in moors, except some information from cultivation studies of the 1970s...
April 11, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28397401/anaerobic-utilization-of-fe-iii-xenosiderophores-among-bacteroides-species-and-the-distinct-assimilation-of-fe-iii-ferrichrome-by-bacteroides-fragilis-within-the-genus
#17
Edson R Rocha, Anna S Krykunivsky
In this study, we show that Bacteroides species utilize Fe(III)-xenosiderophores as the only source of exogenous iron to support growth under iron-limiting conditions in vitro anaerobically. Bacteroides fragilis was the only species able to utilize Fe(III)-ferrichrome while Bacteroides vulgatus ATCC 8482 and Bacteroides thetaiotaomicron VPI 5482 were able to utilize both Fe(III)-enterobactin and Fe(III)-salmochelin S4 as the only source of iron in a dose-dependent manner. We have investigated the way B. fragilis assimilates Fe(III)-ferrichrome as initial model to understand the utilization of xenosiderophores in anaerobes...
April 11, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28397370/conservation-and-diversity-of-the-irre-ddro-controlled-radiation-response-in-radiation-resistant-deinococcus-bacteria
#18
Laurence Blanchard, Philippe Guérin, David Roche, Stéphane Cruveiller, David Pignol, David Vallenet, Jean Armengaud, Arjan de Groot
The extreme radiation resistance of Deinococcus bacteria requires the radiation-stimulated cleavage of protein DdrO by a specific metalloprotease called IrrE. DdrO is the repressor of a predicted radiation/desiccation response (RDR) regulon, composed of radiation-induced genes having a conserved DNA motif (RDRM) in their promoter regions. Here, we showed that addition of zinc ions to purified apo-IrrE, and short exposure of Deinococcus cells to zinc ions, resulted in cleavage of DdrO in vitro and in vivo, respectively...
April 11, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28371510/acuc-a-histone-deacetylase-contributes-to-the-pathogenicity-of-aeromonas-hydrophila
#19
Qingling Jiang, Wenbo Chen, Yingxue Qin, Lixing Huang, Xiaojin Xu, Lingmin Zhao, Qingpi Yan
The interactions of pathogens and phagocytes are complex. Our study demonstrated that Aeromonas hydrophila B11 can survive in the macrophagocytes of Tilapia mossambica. To explore the regulatory processes of A. hydrophila survival in the macrophagocytes, we used the mini-Tn10 transposon mutagenesis system to build a mutant library by mixing Escherichia coli Sm10 (pLOFKm) and A. hydrophila B11. In total, 102 mutant colonies were detected, and 11 of them showed reduced survival in macrophagocytes. The mutant with the most severe phenotype, AM73, was chosen for further research...
March 30, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28371280/response-of-the-rhizosphere-prokaryotic-community-of-barley-hordeum-vulgare-l-to-elevated-atmospheric-co2-concentration-in-open-top-chambers
#20
Márton Szoboszlay, Astrid Näther, Esther Mitterbauer, Jürgen Bender, Hans-Joachim Weigel, Christoph C Tebbe
The effect of elevated atmospheric CO2 concentration [CO2 ] on the diversity and composition of the prokaryotic community inhabiting the rhizosphere of winter barley (Hordeum vulgare L.) was investigated in a field experiment, using open-top chambers. Rhizosphere samples were collected at anthesis (flowering stage) from six chambers with ambient [CO2 ] (approximately 400 ppm) and six chambers with elevated [CO2 ] (700 ppm). The V4 region of the 16S rRNA gene was PCR-amplified from the extracted DNA and sequenced on an Illumina MiSeq instrument...
March 30, 2017: MicrobiologyOpen
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