References of "Frontiers in Microbiology"
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See detailA Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies
Massart, Sebastien; Candresse, Thierry; Gil, Jose et al

in Frontiers in Microbiology (2017), 8(45),

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See detailTemporal dynamics of soil microbial communities below the seedbed under two contrasting tillage regimes
Degrune, Florine; Theodorakopoulos, Nicolas; Colinet, Gilles ULg et al

in Frontiers in Microbiology (2017)

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See detailAssessment of the Potential Role of Streptomyces in Cave Moonmilk Formation
Maciejewska, Marta; Adam, Delphine; Naomé, Aymeric ULg et al

in Frontiers in Microbiology (2017), 8

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See detailComparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium.
Iskandar, Christelle F.; Borges, Frederic; Taminiau, Bernard ULg et al

in Frontiers in Microbiology (2017), 8

Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and ... [more ▼]

Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium. [less ▲]

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See detailKey impact of an uncommon plasmid on bacillus amyloliquefaciens subsp. plantarum S499 developmental traits and lipopeptide production
Molinatto, G.; Franzil, L.; Steels, Sébastien ULg et al

in Frontiers in Microbiology (2017), 8(JAN),

The rhizobacterium Bacillus amyloliquefaciens subsp. plantarum S499 (S499) is particularly efficient in terms of the production of cyclic lipopeptides, which are responsible for the high level of plant ... [more ▼]

The rhizobacterium Bacillus amyloliquefaciens subsp. plantarum S499 (S499) is particularly efficient in terms of the production of cyclic lipopeptides, which are responsible for the high level of plant disease protection provided by this strain. Sequencing of the S499 genome has highlighted genetic differences and similarities with the closely related rhizobacterium B. amyloliquefaciens subsp. plantarum FZB42 (FZB42). More specifically, a rare 8008 bp plasmid (pS499) harboring a rap-phr cassette constitutes a major distinctive element between S499 and FZB42. By curing this plasmid, we demonstrated that its presence is crucial for preserving the typical physiology of S499 cells. Indeed, the growth rate and extracellular proteolytic activity were significantly affected in the cured strain (S499 P-). Furthermore, pS499 made a significant contribution to the regulation of cyclic lipopeptide production. Surfactins and fengycins were produced in higher quantities by S499 P-, whereas lower amounts of iturins were detected. In line with the increase in surfactin release, bacterial motility improved after curing, whereas the ability to form biofilm was reduced in vitro. The antagonistic effect against phytopathogenic fungi was also limited for S499 P-, most probably due to the reduction of iturin production. With the exception of this last aspect, S499 P- behavior fell between that of S499 and FZB42, suggesting a role for the plasmid in shaping some of the phenotypic differences observed in the two strains. © 2017 Molinatto, Franzil, Steels, Puopolo, Pertot and Ongena. [less ▲]

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See detailInsights into abundant rumen ureolytic bacterial community using rumen simulation system
Jin, Di; Zhao, Shengguo; Wang, Pengpeng et al

in Frontiers in Microbiology (2016), 7(1006),

Urea, a non-protein nitrogen for dairy cows, is rapidly hydrolyzed to ammonia by urease produced by ureolytic bacteria in the rumen, and the ammonia is used as nitrogen for rumen bacterial growth. However ... [more ▼]

Urea, a non-protein nitrogen for dairy cows, is rapidly hydrolyzed to ammonia by urease produced by ureolytic bacteria in the rumen, and the ammonia is used as nitrogen for rumen bacterial growth. However, there is limited knowledge with regard to the ureolytic bacteria community in the rumen. To explore the ruminal ureolytic bacterial community, urea, or acetohydroxamic acid (AHA, an inhibitor of urea hydrolysis) were supplemented into the rumen simulation systems. The bacterial 16S rRNA genes were sequenced by Miseq high-throughput sequencing and used to reveal the ureoltyic bacteria by comparing different treatments. The results revealed that urea supplementation significantly increased the ammonia concentration, and AHA addition inhibited urea hydrolysis. Urea supplementation significantly increased the richness of bacterial community and the proportion of ureC genes. The composition of bacterial community following urea or AHA supplementation showed no significant difference compared to the groups without supplementation. The abundance of Bacillus and unclassified Succinivibrionaceae increased significantly following urea supplementation. Pseudomonas, Haemophilus, Neisseria, Streptococcus, and Actinomyces exhibited a positive response to urea supplementation and a negative response to AHA addition. Results retrieved from the NCBI protein database and publications confirmed that the representative bacteria in these genera mentioned above had urease genes or urease activities. Therefore, the rumen ureolytic bacteria were abundant in the genera of Pseudomonas, Haemophilus, Neisseria, Streptococcus, Actinomyces, Bacillus, and unclassified Succinivibrionaceae. Insights into abundant rumen ureolytic bacteria provide the regulation targets to mitigate urea hydrolysis and increase efficiency of urea nitrogen utilization in ruminants. [less ▲]

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See detailBiosynthesis, Chemical Structure, and Structure-Activity Relationship of Orfamide Lipopeptides Produced by Pseudomonas protegens and Related Species
Ma, Zongwang; Geudens, Niels; Kieu, Nam P. et al

in Frontiers in Microbiology (2016), 7

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See detailAerobiology over Antarctica – a new initiative for atmospheric ecology
Pearce, David; Alekhina, Irina; Terauds et al

in Frontiers in Microbiology (2016), 7

The role of aerial dispersal in shaping patterns of biodiversity remains poorly understood, mainly due to a lack of coordinated efforts in gathering data at appropriate temporal and spatial scales. It has ... [more ▼]

The role of aerial dispersal in shaping patterns of biodiversity remains poorly understood, mainly due to a lack of coordinated efforts in gathering data at appropriate temporal and spatial scales. It has been long known that the rate of dispersal to an ecosystem can significantly influence ecosystem dynamics, and that aerial transport has been identified as an important source of biological input to remote locations. With the considerable effort devoted in recent decades to understanding atmospheric circulation in the south-polar region, a unique opportunity has emerged to investigate the atmospheric ecology of Antarctica, from regional to continental scales. This concept note identifies key questions in Antarctic microbial biogeography and the need for standardized sampling and analysis protocols to address such questions. A consortium of polar aerobiologists is established to bring together researchers with a common interest in the airborne dispersion of microbes and other propagules in the Antarctic, with opportunities for comparative studies in the Arctic. [less ▲]

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See detailThe cultivable surface microbiota of the brown alga Ascophyllum nodosum is enriched in macroalgal-polysaccharide-degrading bacteria
Martin, Marjolaine ULg; Barbeyron, Tristan; Martin, Renée ULg et al

in Frontiers in Microbiology (2015), 6(december),

Bacteria degrading algal polysaccharides are key players in the global carbon cycle and in algal biomass recycling. Yet the water column, which has been studied largely by metagenomic approaches, is poor ... [more ▼]

Bacteria degrading algal polysaccharides are key players in the global carbon cycle and in algal biomass recycling. Yet the water column, which has been studied largely by metagenomic approaches, is poor in such bacteria and their algal-polysaccharide-degrading enzymes. Even more surprisingly, the few published studies on seaweed-associated microbiomes have revealed low abundances of such bacteria and their specific enzymes. However, as macroalgal cell-wall polysaccharides do not accumulate in nature, these bacteria and their unique polysaccharidases must not be that uncommon. We, therefore, looked at the polysaccharide-degrading activity of the cultivable bacterial subpopulation associated with Ascophyllum nodosum. From A. nodosum triplicates, 324 bacteria were isolated and taxonomically identified. Out of these isolates, 78 (∼25%) were found to act on at least one tested algal polysaccharide (agar, ι- or κ-carrageenan, or alginate). The isolates “active” on algal-polysaccharides belong to 11 genera: Cellulophaga, Maribacter, Algibacter, and Zobellia in the class Flavobacteriia (41) and Pseudoalteromonas, Vibrio, Cobetia, Shewanella, Colwellia, Marinomonas, and Paraglaceciola in the class Gammaproteobacteria (37). A major part represents likely novel species. Different proportions of bacterial phyla and classes were observed between the isolated cultivable subpopulation and the total microbial community previously identified on other brown algae. Here, Bacteroidetes and Gammaproteobacteria were found to be the most abundant and some phyla (as Planctomycetes and Cyanobacteria) frequently encountered on brown algae weren’t identified. At a lower taxonomic level, twelve genera, well-known to be associated with algae (with the exception for Colwellia), were consistently found on all three A. nosodum samples. Even more interesting, 9 of the 11 above mentioned genera containing polysaccharolytic isolates were predominant in this common core. The cultivable fraction of the bacterial community associated with A. nodosum is, thus, significantly enriched in macroalgal-polysaccharide-degrading bacteria and these bacteria seem important for the seaweed holobiont even though they are under-represented in alga-associated microbiome studies. [less ▲]

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See detailProtection of Antarctic microbial communities–‘out of sight, out of mind’
Hughes, Kevin; Cowan, Don; Wilmotte, Annick ULg

in Frontiers in Microbiology (2015), 6(151), 1-6

RecentadvancesinmolecularbiologytechniqueshaveshownthepresenceofdiversemicrobialcommunitiesandendemicspeciesinAntarctica.Endemicmicrobesmaybeapotentialsourceofnovelbiotechnologicallyimportantcompounds ... [more ▼]

RecentadvancesinmolecularbiologytechniqueshaveshownthepresenceofdiversemicrobialcommunitiesandendemicspeciesinAntarctica.Endemicmicrobesmaybeapotentialsourceofnovelbiotechnologicallyimportantcompounds,including,forexample,newantibiotics.Thus,thescientificandbiotechnologicalvalueofAntarcticterrestrialmicrobialhabitatscanbecompromisedbyhumanvisitationtoagreaterextentthanpreviouslyrealized.Theever-increasinghumanfootprintinAntarcticamakesconsiderationofthistopicmorepressing,asthenumberoflocationsknowntobepristinehabitats,whereincreasinglysophisticatedcutting-edgeresearchtechniquesmaybeusedtotheirfullpotential,declines.ExaminationoftheProtectedAreassystemoftheAntarcticTreatyshowsthatmicrobialhabitatsaregenerallypoorlyprotected.NoothercontinentonEarthisdominatedtothesamedegreebymicrobialspecies,andrealopportunitiesexisttodevelopnewwaysofconceptualizingandimplementingconservationofmicrobialbiogeographyonacontinentalscale.Herewehighlightpotentialthreatsbothtotheconservationofterrestrialmicrobialecosystems,andtofuturescientificresearchrequiringtheirstudy. [less ▲]

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See detailAnti-biofilm activities from marine cold adapted bacteria against staphylococci and Pseudomonas aeruginosa
Papa, R.; Selan, L.; Parrilli, E. et al

in Frontiers in Microbiology (2015), 6

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