Paul Vos | Ghent University (original) (raw)
Papers by Paul Vos
International Journal of Systematic Bacteriology, 1990
International Journal of Systematic Bacteriology, 1998
Paenibacillus azotofixans (Seldin et a/. 1984) Ash et a/. 1995 does not have priority over Paenib... more Paenibacillus azotofixans (Seldin et a/. 1984) Ash et a/. 1995 does not have priority over Paenibacillus dururn (Smith and Cat0 1974) Collins et a/.
Genome announcements, Jan 2, 2015
We report the draft genome sequence of Pseudomonas sp. nov. H2, isolated from creek sediment in M... more We report the draft genome sequence of Pseudomonas sp. nov. H2, isolated from creek sediment in Moscow, ID, USA. The strain is most closely related to Pseudomonas putida. However, it has a slightly smaller genome that appears to have been impacted by horizontal gene transfer and poorly maintains IncP-1 plasmids.
Applied and environmental microbiology, Jan 26, 2014
In recent years, the frequent detection of the banned thyreostat, thiouracil (TU), in livestock u... more In recent years, the frequent detection of the banned thyreostat, thiouracil (TU), in livestock urine has been related to endogenous TU formation following digestion of glucosinolate-rich Brassicaceae crops. Recently, it was demonstrated that fecal bacteria upon in vitro digestion of Brassicaceae, induce TU detection in livestock (porcines > bovines). Therefore, the present study intended to isolate and identify bacteria involved in this intestinal TU formation upon Brassicaceae digestion, and gain more insight in the underlying mechanism in porcines. Twenty porcine fecal inocula (gilts-multiparous sows) were assessed through static in vitro colonic digestion simulations with rapeseed. After derivatisation and extraction of the fecal suspensions, TU was analysed using LC-MS(2). On average lower TU concentrations were observed in fecal colonic simulations in gilts (8.35 ± 3.42 SD ng g(-1) rapeseed) in comparison to multiparous sows (52.63 ng g(-1) ± 16.17 SD), which correlates wit...
Aquaculture, 2015
Vibrios belonging to the Harveyi clade are important pathogens of a large number of marine animal... more Vibrios belonging to the Harveyi clade are important pathogens of a large number of marine animals in the aquaculture industry. In this study, six isolates (H1 to H6) were obtained from a shrimp hatchery in Rio Grande do Norte (Natal-Area, Brazil), which had been confronted with disease outbreaks in 2009. The aim was to characterize the virulence of these isolates, both in vitro (virulence factor production) and in vivo (virulence towards gnotobiotic brine shrimp, Artemia franciscana, larvae) and to compare these characteristics to those of the most virulent pathogen in the brine shrimp model described to date, Vibrio campbellii LMG 21363. Of all 6 isolates, H5 and H6 were found to be the most virulent ones and were therefore selected for further characterization. Isolate H5 exhibited a similar virulence as the control strain, while H6 exhibited a higher virulence, both in gnotobiotic and conventionally reared brine shrimp. Both H5 and H6 were motile and produced all of the lytic enzymes tested (hemolysin, caseinase, gelatinase, lipase and phospholipase). Although H6 was the most virulent isolate in vivo, this was not reflected in the highest production of all virulence factors tested. Finally, isolates H5 and H6 were identified to belong to the Harveyi clade of vibrios.
PLoS ONE, 2012
Worldwide, Dickeya (formerly Erwinia chrysanthemi) is causing soft rot diseases on a large divers... more Worldwide, Dickeya (formerly Erwinia chrysanthemi) is causing soft rot diseases on a large diversity of crops and ornamental plants. Strains affecting potato are mainly found in D. dadantii, D. dianthicola and D. zeae, which appear to have a marked geographical distribution. Furthermore, a few Dickeya isolates from potato are attributed to D. chrysanthemi and D. dieffenbachiae. In Europe, isolates of Erwinia chrysanthemi biovar 1 and biovar 7 from potato are now classified in D. dianthicola. However, in the past few years, a new Dickeya biovar 3 variant, tentatively named 'Dickeya solani', has emerged as a common major threat, in particular in seed potatoes. Sequences of a fliC gene fragment were used to generate a phylogeny of Dickeya reference strains from culture collections and with this reference backbone, to classify pectinolytic isolates, i.e. Dickeya spp. from potato and ornamental plants. The reference strains of the currently recognized Dickeya species and 'D. solani' were unambiguously delineated in the fliC phylogram. D. dadantii, D. dianthicola and 'D. solani' displayed unbranched clades, while D. chrysanthemi, D. zeae and D. dieffenbachiae branched into subclades and lineages. Moreover, Dickeya isolates from diagnostic samples, in particular biovar 3 isolates from greenhouse ornamentals, formed several new lineages. Most of these isolates were positioned between the clade of 'D. solani' and D. dadantii as transition variants. New lineages also appeared in D. dieffenbachiae and in D. zeae. The strains and isolates of D. dianthicola and 'D. solani' were differentiated by a fliC sequence useful for barcode identification. A fliC TaqManHreal-time PCR was developed for 'D. solani' and the assay was provisionally evaluated in direct analysis of diagnostic potato samples. This molecular tool can support the efforts to control this particular phytopathogen in seed potato certification.
PLoS ONE, 2013
Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The scie... more Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The scientific outcome of short read sequencing studies therefore alters with the gene region sequenced. We wanted to gain insight in the impact of primer choice on the outcome of short read sequencing efforts. All the unknowns associated with sequencing data, i.e. primer coverage rate, phylogeny, OTU-richness and taxonomic assignment, were therefore implemented in one study for ten well established universal primers (338f/r, 518f/r, 799f/r, 926f/r and 1062f/r) targeting dispersed regions of the bacterial 16S rRNA gene. All analyses were performed on nearly full length and in silico generated short read sequence libraries containing 1175 sequences that were carefully chosen as to present a representative substitute of the SILVA SSU database. The 518f and 799r primers, targeting the V4 region of the 16S rRNA gene, were found to be particularly suited for short read sequencing studies, while the primer 1062r, targeting V6, seemed to be least reliable. Our results will assist scientists in considering whether the best option for their study is to select the most informative primer, or the primer that excludes interferences by host-organelle DNA. The methodology followed can be extrapolated to other primers, allowing their evaluation prior to the experiment.
PLoS ONE, 2012
Knowledge on long-term preservation of microorganisms is limited and research in the field is sca... more Knowledge on long-term preservation of microorganisms is limited and research in the field is scarce despite its importance for microbial biodiversity and biotechnological innovation. Preservation of fastidious organisms such as methane-oxidizing bacteria (MOB) has proven difficult. Most MOB do not survive lyophilization and only some can be cryopreserved successfully for short periods. A large-scale study was designed for a diverse set of MOB applying fifteen cryopreservation or lyophilization conditions. After three, six and twelve months of preservation, the viability (via live-dead flow cytometry) and culturability (via most-probable number analysis and plating) of the cells were assessed. All strains could be cryopreserved without a significant loss in culturability using 1% trehalose in 10-fold diluted TSB (TT) as preservation medium and 5% DMSO as cryoprotectant. Several other cryopreservation and lyophilization conditions, all of which involved the use of TT medium, also allowed successful preservation but showed a considerable loss in culturability. We demonstrate here that most of these non-culturables survived preservation according to viability assessment indicating that preservation induces a viable but non-culturable (VBNC) state in a significant fraction of cells. Since this state is reversible, these findings have major implications shifting the emphasis from survival to revival of cells in a preservation protocol. We showed that MOB cells could be significantly resuscitated from the VBNC state using the TT preservation medium.
Microbiology, 2013
The last decade has shown an increased interest in the utilization of bacteria for applications r... more The last decade has shown an increased interest in the utilization of bacteria for applications ranging from bioremediation to wastewater purification and promotion of plant growth. In order to extend the current number of microorganism mediated applications, a continued quest for new agents is required. This study focused on the genus Pseudomonas, which is known to harbour strains with a very diverse set of interesting properties. The aim was to identify growth media that allow retrieval of a high Pseudomonas diversity, as such increasing the chance of isolating isolates with beneficial properties. Three cultivation media: trypticase soy agar (TSA), potato dextrose agar (PDA) and Pseudomonas isolation agar (PIA) were evaluated for their abilities to grow Pseudomonas strains. TSA and PDA were found to generate the largest Pseudomonas diversity. However, communities obtained with both media overlapped. Communities obtained with PIA, on the other hand, were unique. This indicated that the largest diversity is obtained by sampling from either PDA or TSA and from PIA in parallel. To evaluate biodiversity of the isolated Pseudomonas members on the media, an appropriate biomarker had to be identified. Hence, an introductory investigation of the taxonomic resolution of the 16S rRNA, rpoD, gyrB and rpoB genes was performed. The rpoD gene sequences not only had a high phylogenetic content and the highest taxonomic resolution amongst the genes investigated, it also had a gene phylogeny that related well with that of the 16S rRNA gene.
International Journal of Systematic and Evolutionary Microbiology, 2007
A novel gliding, heterotrophic, Gram-negative, yellow–orange-pigmented, aerobic, oxidase- and cat... more A novel gliding, heterotrophic, Gram-negative, yellow–orange-pigmented, aerobic, oxidase- and catalase-positive bacterium, designated strain KMM 6151T, was isolated from the Pacific red alga Polysiphonia japonica. Analysis of the 16S rRNA gene sequence of the strain revealed that it formed a distinct lineage within the genus Maribacter, family Flavobacteriaceae, with sequence similarities in the range 94.6–96.9 %. On the basis of phenotypic, genotypic and phylogenetic data, strain KMM 6151T represents a novel species of the genus Maribacter, for which the name Maribacter polysiphoniae sp. nov. is proposed. The type strain is KMM 6151T (=KCTC 22021T=LMG 23671T).
FEMS Yeast Research, 2009
The fermentation of the Theobroma cacao beans, involving yeasts, lactic acid bacteria, and acetic... more The fermentation of the Theobroma cacao beans, involving yeasts, lactic acid bacteria, and acetic acid bacteria, has a major influence on the quality of the resulting cocoa. An assessment of the microbial community of cocoa bean heap fermentations in Ghana resulted in 91 yeast isolates. These were grouped by PCRfingerprinting with the primer M13. Representative isolates were identified using the D1/D2 region of the large subunit rRNA gene, internal transcribed spacer sequences and partial actin gene sequences leading to the detection of 15 species. Properties of importance for cocoa bean fermentation, namely sucrose, glucose, and citrate assimilation capacity, pH-, ethanol-, and heat-tolerance, were examined for selected isolates. Pichia kudriavzevii (Issatchenkia orientalis), Saccharomyces cerevisiae, and Hanseniaspora opuntiae formed the major components of the yeast community. Hanseniaspora opuntiae was identified conclusively for the first time from cocoa fermentations. Among the less frequently encountered species, Candida carpophila, Candida orthopsilosis, Kodamaea ohmeri, Meyerozyma (Pichia) caribbica, Pichia manshurica, Saccharomycodes ludwigii, and Yamadazyma (Pichia) mexicana were not yet documented from this substrate. Hanseniaspora opuntiae was preferably growing during the earlier phase of fermentation, reflecting its tolerance to low pH and its citrate-negative phenotype, while no specific temporal distribution was recognized for P. kudriavzevii and S. cerevisiae.
FEMS Microbiology Ecology, 1999
The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is known to inhibit methanotrophic bacteria.... more The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is known to inhibit methanotrophic bacteria. Methane oxidation was therefore used as a parameter to evaluate the residual 2,4-D after bioaugmentation of an agricultural soil. Several strains harbouring catabolic plasmids which code for the degradation of this pesticide, were compared for their potential to alleviate the negative impact of 2,4-D on methane oxidation by soil microorganisms. Three indigenous soil bacteria which contain the 2,4-D degradative plasmid pEMT1k, obtained from a donor by in situ plasmid transfer in previous experiments, were compared with Ralstonia eutropha JMP134, which harbours the well studied 2,4-D degradative plasmid pJP4. In addition a Pseudomonas putida UWC3(pEMT1k), which does not degrade 2,4-D, was used as donor to investigate the potential bioaugmentation through in situ transfer of the catabolic genes towards the indigenous soil bacteria. Both the strains that can degrade 2,4-D as well as the P. putida donor strain could enhance the recovery of methane oxidation by increasing the rate of degradation of 2,4-D and thus removing its toxic effect on the methane oxidising microbial populations. In all cases the time needed to oxidise methane was consistently shorter (4^10 days) in a 2,4-D treated soil inoculated with the strains, than in the non-inoculated 2,4-D treated soil, but still longer (5^10 days) than in the soil without 2,4-D. These data indicate that pesticide residues as well as their toxic effect on important soil microbial processes could be successfully removed from the soil by addition of well adapted specialised strains with the genetic information required to degrade the applied pesticides.
Engineering in Life Sciences, 2007
The breakthroughs in microbiology have allowed us to come to terms with the microbial resources p... more The breakthroughs in microbiology have allowed us to come to terms with the microbial resources present in culture collections and in natural environments. The challenge at present is to manage these microbial resources, particularly when one deals with open systems where the dynamics of microbial ecology are predominant. Hence, to properly address the aspects of Microbial Resource Management (MRM), one needs to handle the questions of who is there, who is doing what with whom and how can one adjust, control and/or steer these mixed cultures and communities. It is argued that microbial ecologists and environmental microbiologists need to address a new mind‐set. The Beijerinck axioma that all microorganisms are everywhere should not be presumed to be generally valid. The Darwin based niche assembly concept needs to be supplemented with the neutral theory of Hubbell. The Pareto 80/20 principle is also applicable to the macro‐economies of microbial communities. Finally, the concept of ...
BMC Microbiology, 2014
Background: The currently accepted thesis on nitrogenous fertilizer additions on methane oxidatio... more Background: The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. Results: We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Conclusions: Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.
BMC Microbiology, 2013
Background: Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker... more Background: Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker in tomato. Cmm is present nearly in all European countries. During the last three years several local outbreaks were detected in Belgium. The lack of a convenient high-resolution strain-typing method has hampered the study of the routes of transmission of Cmm and epidemiology in tomato cultivation. In this study the genetic relatedness among a worldwide collection of Cmm strains and their relatives was approached by gyrB and dnaA gene sequencing. Further, we developed and applied a multilocus variable number of tandem repeats analysis (MLVA) scheme to discriminate among Cmm strains. Results: A phylogenetic analysis of gyrB and dnaA gene sequences of 56 Cmm strains demonstrated that Belgian Cmm strains from recent outbreaks of 2010-2012 form a genetically uniform group within the Cmm clade, and Cmm is phylogenetically distinct from other Clavibacter subspecies and from non-pathogenic Clavibacter-like strains. MLVA conducted with eight minisatellite loci detected 25 haplotypes within Cmm. All strains from Belgian outbreaks, isolated between 2010 and 2012, together with two French strains from 2010 seem to form one monomorphic group. Regardless of the isolation year, location or tomato cultivar, Belgian strains from recent outbreaks belonged to the same haplotype. On the contrary, strains from diverse geographical locations or isolated over longer periods of time formed mostly singletons. Conclusions: We hypothesise that the introduction might have originated from one lot of seeds or contaminated tomato seedlings that was the source of the outbreak in 2010 and that these Cmm strains persisted and induced infection in 2011 and 2012. Our results demonstrate that MLVA is a promising typing technique for a local surveillance and outbreaks investigation in epidemiological studies of Cmm.
Applied and Environmental Microbiology, 2011
Chloropropham-degrading cultures were obtained from sludge and soil samples by using two differen... more Chloropropham-degrading cultures were obtained from sludge and soil samples by using two different enrichment techniques: (i) planktonic enrichments in shaken liquid medium and (ii) biofilm enrichments on two types of solid matrixes (plastic chips and gravel). Denaturing gradient gel electrophoresis fingerprinting showed that planktonic and biofilm cultures had a different community composition depending on the presence and type of added solid matrix during enrichment. This was reflected in the unique chloropropham-degrading species that could be isolated from the different cultures. Planktonic and biofilm cultures also differed in chloropropham-degrading activity. With biofilm cultures, slower chloropropham removal was observed, but with less build-up of the toxic intermediate 3-chloroaniline. Disruption of the biofilm architecture resulted in degradation characteristics shifting toward those of the free suspensions, indicating the importance of a well-established biofilm structure...
Applied and Environmental Microbiology, 2000
Transfer of the 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids pEMT1 and pJP4 from a... more Transfer of the 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids pEMT1 and pJP4 from an introduced donor strain, Pseudomonas putida UWC3, to the indigenous bacteria of two different horizons (A horizon, depth of 0 to 30 cm; B horizon, depth of 30 to 60 cm) of a 2,4-D-contaminated soil was investigated as a means of bioaugmentation. When the soil was amended with nutrients, plasmid transfer and enhanced degradation of 2,4-D were observed. These findings were most striking in the B horizon, where the indigenous bacteria were unable to degrade any of the 2,4-D (100 mg/kg of soil) during at least 22 days but where inoculation with either of the two plasmid donors resulted in complete 2,4-D degradation within 14 days. In contrast, in soils not amended with nutrients, inoculation of donors in the A horizon and subsequent formation of transconjugants (10 5 CFU/g of soil) could not increase the 2,4-D degradation rate compared to that of the noninoculated soil. However, donor inoc...
![Research paper thumbnail of Isolation and Characterization of Human Intestinal Bacteria Capable of Transforming the Dietary Carcinogen 2-Amino-1-Methyl-6-Phenylimidazo[4,5- b ]Pyridine](https://attachments.academia-assets.com/118711338/thumbnails/1.jpg)
](Applied and Environmental Microbiology, 2008
2-Amino-1-methyl-6-phenylimidazo[4,5- b ]pyridine (PhIP) is a carcinogenic heterocyclic aromatic ... more 2-Amino-1-methyl-6-phenylimidazo[4,5- b ]pyridine (PhIP) is a carcinogenic heterocyclic aromatic amine formed in meat products during cooking. Although the formation of hazardous PhIP metabolites by mammalian enzymes has been extensively reported, research on the putative involvement of the human intestinal microbiota in PhIP metabolism remains scarce. In this study, the in vitro conversion of PhIP into its microbial derivate, 7-hydroxy-5-methyl-3-phenyl-6,7,8,9-tetrahydropyrido[3′,2′:4,5]imidazo[1,2- a ]pyrimidin-5-ium chloride (PhIP-M1), by fecal samples from 18 human volunteers was investigated. High-performance liquid chromatography analysis showed that all human fecal samples transformed PhIP but with efficiencies ranging from 1.8 to 96% after 72 h of incubation. Two PhIP-transforming strains, PhIP-M1-a and PhIP-M1-b, were isolated from human feces and identified by fluorescent amplified fragment length polymorphism and pheS sequence analyses as Enterococcus faecium strains. So...
Análisis de especies de Pseudomonas fitopatógenas usando métodos inteligentes de aprendizaje: un ... more Análisis de especies de Pseudomonas fitopatógenas usando métodos inteligentes de aprendizaje: un enfoque general sobre taxonomía y análisis de ácidos grasos dentro del género
BMC Genomics, 2013
Background Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine org... more Background Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus Xanthomonas, and known for its host specificity. As part of a broader pathogenicity study, the genome of a Belgian, virulent Xf strain (LMG 25863) was assembled to draft status and examined for its pathogenicity related gene content. Results The Xf draft genome (4.2 Mb) was considerably smaller than most known Xanthomonas genomes (~5 Mb). Only half of the genes coding for TonB-dependent transporters and cell-wall degrading enzymes that are typically present in other Xanthomonas genomes, were found in Xf. Other missing genes/regions with a possible impact on its plant-host interaction were: i) the three loci for xylan degradation and metabolism, ii) a locus coding for a ß-ketoadipate phenolics catabolism pathway, iii) xcs, one of two Type II Secretion System coding regions in Xant...
International Journal of Systematic Bacteriology, 1990
International Journal of Systematic Bacteriology, 1998
Paenibacillus azotofixans (Seldin et a/. 1984) Ash et a/. 1995 does not have priority over Paenib... more Paenibacillus azotofixans (Seldin et a/. 1984) Ash et a/. 1995 does not have priority over Paenibacillus dururn (Smith and Cat0 1974) Collins et a/.
Genome announcements, Jan 2, 2015
We report the draft genome sequence of Pseudomonas sp. nov. H2, isolated from creek sediment in M... more We report the draft genome sequence of Pseudomonas sp. nov. H2, isolated from creek sediment in Moscow, ID, USA. The strain is most closely related to Pseudomonas putida. However, it has a slightly smaller genome that appears to have been impacted by horizontal gene transfer and poorly maintains IncP-1 plasmids.
Applied and environmental microbiology, Jan 26, 2014
In recent years, the frequent detection of the banned thyreostat, thiouracil (TU), in livestock u... more In recent years, the frequent detection of the banned thyreostat, thiouracil (TU), in livestock urine has been related to endogenous TU formation following digestion of glucosinolate-rich Brassicaceae crops. Recently, it was demonstrated that fecal bacteria upon in vitro digestion of Brassicaceae, induce TU detection in livestock (porcines > bovines). Therefore, the present study intended to isolate and identify bacteria involved in this intestinal TU formation upon Brassicaceae digestion, and gain more insight in the underlying mechanism in porcines. Twenty porcine fecal inocula (gilts-multiparous sows) were assessed through static in vitro colonic digestion simulations with rapeseed. After derivatisation and extraction of the fecal suspensions, TU was analysed using LC-MS(2). On average lower TU concentrations were observed in fecal colonic simulations in gilts (8.35 ± 3.42 SD ng g(-1) rapeseed) in comparison to multiparous sows (52.63 ng g(-1) ± 16.17 SD), which correlates wit...
Aquaculture, 2015
Vibrios belonging to the Harveyi clade are important pathogens of a large number of marine animal... more Vibrios belonging to the Harveyi clade are important pathogens of a large number of marine animals in the aquaculture industry. In this study, six isolates (H1 to H6) were obtained from a shrimp hatchery in Rio Grande do Norte (Natal-Area, Brazil), which had been confronted with disease outbreaks in 2009. The aim was to characterize the virulence of these isolates, both in vitro (virulence factor production) and in vivo (virulence towards gnotobiotic brine shrimp, Artemia franciscana, larvae) and to compare these characteristics to those of the most virulent pathogen in the brine shrimp model described to date, Vibrio campbellii LMG 21363. Of all 6 isolates, H5 and H6 were found to be the most virulent ones and were therefore selected for further characterization. Isolate H5 exhibited a similar virulence as the control strain, while H6 exhibited a higher virulence, both in gnotobiotic and conventionally reared brine shrimp. Both H5 and H6 were motile and produced all of the lytic enzymes tested (hemolysin, caseinase, gelatinase, lipase and phospholipase). Although H6 was the most virulent isolate in vivo, this was not reflected in the highest production of all virulence factors tested. Finally, isolates H5 and H6 were identified to belong to the Harveyi clade of vibrios.
PLoS ONE, 2012
Worldwide, Dickeya (formerly Erwinia chrysanthemi) is causing soft rot diseases on a large divers... more Worldwide, Dickeya (formerly Erwinia chrysanthemi) is causing soft rot diseases on a large diversity of crops and ornamental plants. Strains affecting potato are mainly found in D. dadantii, D. dianthicola and D. zeae, which appear to have a marked geographical distribution. Furthermore, a few Dickeya isolates from potato are attributed to D. chrysanthemi and D. dieffenbachiae. In Europe, isolates of Erwinia chrysanthemi biovar 1 and biovar 7 from potato are now classified in D. dianthicola. However, in the past few years, a new Dickeya biovar 3 variant, tentatively named 'Dickeya solani', has emerged as a common major threat, in particular in seed potatoes. Sequences of a fliC gene fragment were used to generate a phylogeny of Dickeya reference strains from culture collections and with this reference backbone, to classify pectinolytic isolates, i.e. Dickeya spp. from potato and ornamental plants. The reference strains of the currently recognized Dickeya species and 'D. solani' were unambiguously delineated in the fliC phylogram. D. dadantii, D. dianthicola and 'D. solani' displayed unbranched clades, while D. chrysanthemi, D. zeae and D. dieffenbachiae branched into subclades and lineages. Moreover, Dickeya isolates from diagnostic samples, in particular biovar 3 isolates from greenhouse ornamentals, formed several new lineages. Most of these isolates were positioned between the clade of 'D. solani' and D. dadantii as transition variants. New lineages also appeared in D. dieffenbachiae and in D. zeae. The strains and isolates of D. dianthicola and 'D. solani' were differentiated by a fliC sequence useful for barcode identification. A fliC TaqManHreal-time PCR was developed for 'D. solani' and the assay was provisionally evaluated in direct analysis of diagnostic potato samples. This molecular tool can support the efforts to control this particular phytopathogen in seed potato certification.
PLoS ONE, 2013
Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The scie... more Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The scientific outcome of short read sequencing studies therefore alters with the gene region sequenced. We wanted to gain insight in the impact of primer choice on the outcome of short read sequencing efforts. All the unknowns associated with sequencing data, i.e. primer coverage rate, phylogeny, OTU-richness and taxonomic assignment, were therefore implemented in one study for ten well established universal primers (338f/r, 518f/r, 799f/r, 926f/r and 1062f/r) targeting dispersed regions of the bacterial 16S rRNA gene. All analyses were performed on nearly full length and in silico generated short read sequence libraries containing 1175 sequences that were carefully chosen as to present a representative substitute of the SILVA SSU database. The 518f and 799r primers, targeting the V4 region of the 16S rRNA gene, were found to be particularly suited for short read sequencing studies, while the primer 1062r, targeting V6, seemed to be least reliable. Our results will assist scientists in considering whether the best option for their study is to select the most informative primer, or the primer that excludes interferences by host-organelle DNA. The methodology followed can be extrapolated to other primers, allowing their evaluation prior to the experiment.
PLoS ONE, 2012
Knowledge on long-term preservation of microorganisms is limited and research in the field is sca... more Knowledge on long-term preservation of microorganisms is limited and research in the field is scarce despite its importance for microbial biodiversity and biotechnological innovation. Preservation of fastidious organisms such as methane-oxidizing bacteria (MOB) has proven difficult. Most MOB do not survive lyophilization and only some can be cryopreserved successfully for short periods. A large-scale study was designed for a diverse set of MOB applying fifteen cryopreservation or lyophilization conditions. After three, six and twelve months of preservation, the viability (via live-dead flow cytometry) and culturability (via most-probable number analysis and plating) of the cells were assessed. All strains could be cryopreserved without a significant loss in culturability using 1% trehalose in 10-fold diluted TSB (TT) as preservation medium and 5% DMSO as cryoprotectant. Several other cryopreservation and lyophilization conditions, all of which involved the use of TT medium, also allowed successful preservation but showed a considerable loss in culturability. We demonstrate here that most of these non-culturables survived preservation according to viability assessment indicating that preservation induces a viable but non-culturable (VBNC) state in a significant fraction of cells. Since this state is reversible, these findings have major implications shifting the emphasis from survival to revival of cells in a preservation protocol. We showed that MOB cells could be significantly resuscitated from the VBNC state using the TT preservation medium.
Microbiology, 2013
The last decade has shown an increased interest in the utilization of bacteria for applications r... more The last decade has shown an increased interest in the utilization of bacteria for applications ranging from bioremediation to wastewater purification and promotion of plant growth. In order to extend the current number of microorganism mediated applications, a continued quest for new agents is required. This study focused on the genus Pseudomonas, which is known to harbour strains with a very diverse set of interesting properties. The aim was to identify growth media that allow retrieval of a high Pseudomonas diversity, as such increasing the chance of isolating isolates with beneficial properties. Three cultivation media: trypticase soy agar (TSA), potato dextrose agar (PDA) and Pseudomonas isolation agar (PIA) were evaluated for their abilities to grow Pseudomonas strains. TSA and PDA were found to generate the largest Pseudomonas diversity. However, communities obtained with both media overlapped. Communities obtained with PIA, on the other hand, were unique. This indicated that the largest diversity is obtained by sampling from either PDA or TSA and from PIA in parallel. To evaluate biodiversity of the isolated Pseudomonas members on the media, an appropriate biomarker had to be identified. Hence, an introductory investigation of the taxonomic resolution of the 16S rRNA, rpoD, gyrB and rpoB genes was performed. The rpoD gene sequences not only had a high phylogenetic content and the highest taxonomic resolution amongst the genes investigated, it also had a gene phylogeny that related well with that of the 16S rRNA gene.
International Journal of Systematic and Evolutionary Microbiology, 2007
A novel gliding, heterotrophic, Gram-negative, yellow–orange-pigmented, aerobic, oxidase- and cat... more A novel gliding, heterotrophic, Gram-negative, yellow–orange-pigmented, aerobic, oxidase- and catalase-positive bacterium, designated strain KMM 6151T, was isolated from the Pacific red alga Polysiphonia japonica. Analysis of the 16S rRNA gene sequence of the strain revealed that it formed a distinct lineage within the genus Maribacter, family Flavobacteriaceae, with sequence similarities in the range 94.6–96.9 %. On the basis of phenotypic, genotypic and phylogenetic data, strain KMM 6151T represents a novel species of the genus Maribacter, for which the name Maribacter polysiphoniae sp. nov. is proposed. The type strain is KMM 6151T (=KCTC 22021T=LMG 23671T).
FEMS Yeast Research, 2009
The fermentation of the Theobroma cacao beans, involving yeasts, lactic acid bacteria, and acetic... more The fermentation of the Theobroma cacao beans, involving yeasts, lactic acid bacteria, and acetic acid bacteria, has a major influence on the quality of the resulting cocoa. An assessment of the microbial community of cocoa bean heap fermentations in Ghana resulted in 91 yeast isolates. These were grouped by PCRfingerprinting with the primer M13. Representative isolates were identified using the D1/D2 region of the large subunit rRNA gene, internal transcribed spacer sequences and partial actin gene sequences leading to the detection of 15 species. Properties of importance for cocoa bean fermentation, namely sucrose, glucose, and citrate assimilation capacity, pH-, ethanol-, and heat-tolerance, were examined for selected isolates. Pichia kudriavzevii (Issatchenkia orientalis), Saccharomyces cerevisiae, and Hanseniaspora opuntiae formed the major components of the yeast community. Hanseniaspora opuntiae was identified conclusively for the first time from cocoa fermentations. Among the less frequently encountered species, Candida carpophila, Candida orthopsilosis, Kodamaea ohmeri, Meyerozyma (Pichia) caribbica, Pichia manshurica, Saccharomycodes ludwigii, and Yamadazyma (Pichia) mexicana were not yet documented from this substrate. Hanseniaspora opuntiae was preferably growing during the earlier phase of fermentation, reflecting its tolerance to low pH and its citrate-negative phenotype, while no specific temporal distribution was recognized for P. kudriavzevii and S. cerevisiae.
FEMS Microbiology Ecology, 1999
The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is known to inhibit methanotrophic bacteria.... more The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is known to inhibit methanotrophic bacteria. Methane oxidation was therefore used as a parameter to evaluate the residual 2,4-D after bioaugmentation of an agricultural soil. Several strains harbouring catabolic plasmids which code for the degradation of this pesticide, were compared for their potential to alleviate the negative impact of 2,4-D on methane oxidation by soil microorganisms. Three indigenous soil bacteria which contain the 2,4-D degradative plasmid pEMT1k, obtained from a donor by in situ plasmid transfer in previous experiments, were compared with Ralstonia eutropha JMP134, which harbours the well studied 2,4-D degradative plasmid pJP4. In addition a Pseudomonas putida UWC3(pEMT1k), which does not degrade 2,4-D, was used as donor to investigate the potential bioaugmentation through in situ transfer of the catabolic genes towards the indigenous soil bacteria. Both the strains that can degrade 2,4-D as well as the P. putida donor strain could enhance the recovery of methane oxidation by increasing the rate of degradation of 2,4-D and thus removing its toxic effect on the methane oxidising microbial populations. In all cases the time needed to oxidise methane was consistently shorter (4^10 days) in a 2,4-D treated soil inoculated with the strains, than in the non-inoculated 2,4-D treated soil, but still longer (5^10 days) than in the soil without 2,4-D. These data indicate that pesticide residues as well as their toxic effect on important soil microbial processes could be successfully removed from the soil by addition of well adapted specialised strains with the genetic information required to degrade the applied pesticides.
Engineering in Life Sciences, 2007
The breakthroughs in microbiology have allowed us to come to terms with the microbial resources p... more The breakthroughs in microbiology have allowed us to come to terms with the microbial resources present in culture collections and in natural environments. The challenge at present is to manage these microbial resources, particularly when one deals with open systems where the dynamics of microbial ecology are predominant. Hence, to properly address the aspects of Microbial Resource Management (MRM), one needs to handle the questions of who is there, who is doing what with whom and how can one adjust, control and/or steer these mixed cultures and communities. It is argued that microbial ecologists and environmental microbiologists need to address a new mind‐set. The Beijerinck axioma that all microorganisms are everywhere should not be presumed to be generally valid. The Darwin based niche assembly concept needs to be supplemented with the neutral theory of Hubbell. The Pareto 80/20 principle is also applicable to the macro‐economies of microbial communities. Finally, the concept of ...
BMC Microbiology, 2014
Background: The currently accepted thesis on nitrogenous fertilizer additions on methane oxidatio... more Background: The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. Results: We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Conclusions: Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.
BMC Microbiology, 2013
Background: Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker... more Background: Clavibacter michiganensis subsp. michiganensis (Cmm) causes bacterial wilt and canker in tomato. Cmm is present nearly in all European countries. During the last three years several local outbreaks were detected in Belgium. The lack of a convenient high-resolution strain-typing method has hampered the study of the routes of transmission of Cmm and epidemiology in tomato cultivation. In this study the genetic relatedness among a worldwide collection of Cmm strains and their relatives was approached by gyrB and dnaA gene sequencing. Further, we developed and applied a multilocus variable number of tandem repeats analysis (MLVA) scheme to discriminate among Cmm strains. Results: A phylogenetic analysis of gyrB and dnaA gene sequences of 56 Cmm strains demonstrated that Belgian Cmm strains from recent outbreaks of 2010-2012 form a genetically uniform group within the Cmm clade, and Cmm is phylogenetically distinct from other Clavibacter subspecies and from non-pathogenic Clavibacter-like strains. MLVA conducted with eight minisatellite loci detected 25 haplotypes within Cmm. All strains from Belgian outbreaks, isolated between 2010 and 2012, together with two French strains from 2010 seem to form one monomorphic group. Regardless of the isolation year, location or tomato cultivar, Belgian strains from recent outbreaks belonged to the same haplotype. On the contrary, strains from diverse geographical locations or isolated over longer periods of time formed mostly singletons. Conclusions: We hypothesise that the introduction might have originated from one lot of seeds or contaminated tomato seedlings that was the source of the outbreak in 2010 and that these Cmm strains persisted and induced infection in 2011 and 2012. Our results demonstrate that MLVA is a promising typing technique for a local surveillance and outbreaks investigation in epidemiological studies of Cmm.
Applied and Environmental Microbiology, 2011
Chloropropham-degrading cultures were obtained from sludge and soil samples by using two differen... more Chloropropham-degrading cultures were obtained from sludge and soil samples by using two different enrichment techniques: (i) planktonic enrichments in shaken liquid medium and (ii) biofilm enrichments on two types of solid matrixes (plastic chips and gravel). Denaturing gradient gel electrophoresis fingerprinting showed that planktonic and biofilm cultures had a different community composition depending on the presence and type of added solid matrix during enrichment. This was reflected in the unique chloropropham-degrading species that could be isolated from the different cultures. Planktonic and biofilm cultures also differed in chloropropham-degrading activity. With biofilm cultures, slower chloropropham removal was observed, but with less build-up of the toxic intermediate 3-chloroaniline. Disruption of the biofilm architecture resulted in degradation characteristics shifting toward those of the free suspensions, indicating the importance of a well-established biofilm structure...
Applied and Environmental Microbiology, 2000
Transfer of the 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids pEMT1 and pJP4 from a... more Transfer of the 2,4-dichlorophenoxyacetic acid (2,4-D) degradation plasmids pEMT1 and pJP4 from an introduced donor strain, Pseudomonas putida UWC3, to the indigenous bacteria of two different horizons (A horizon, depth of 0 to 30 cm; B horizon, depth of 30 to 60 cm) of a 2,4-D-contaminated soil was investigated as a means of bioaugmentation. When the soil was amended with nutrients, plasmid transfer and enhanced degradation of 2,4-D were observed. These findings were most striking in the B horizon, where the indigenous bacteria were unable to degrade any of the 2,4-D (100 mg/kg of soil) during at least 22 days but where inoculation with either of the two plasmid donors resulted in complete 2,4-D degradation within 14 days. In contrast, in soils not amended with nutrients, inoculation of donors in the A horizon and subsequent formation of transconjugants (10 5 CFU/g of soil) could not increase the 2,4-D degradation rate compared to that of the noninoculated soil. However, donor inoc...
Applied and Environmental Microbiology, 2008
2-Amino-1-methyl-6-phenylimidazo[4,5- b ]pyridine (PhIP) is a carcinogenic heterocyclic aromatic ... more 2-Amino-1-methyl-6-phenylimidazo[4,5- b ]pyridine (PhIP) is a carcinogenic heterocyclic aromatic amine formed in meat products during cooking. Although the formation of hazardous PhIP metabolites by mammalian enzymes has been extensively reported, research on the putative involvement of the human intestinal microbiota in PhIP metabolism remains scarce. In this study, the in vitro conversion of PhIP into its microbial derivate, 7-hydroxy-5-methyl-3-phenyl-6,7,8,9-tetrahydropyrido[3′,2′:4,5]imidazo[1,2- a ]pyrimidin-5-ium chloride (PhIP-M1), by fecal samples from 18 human volunteers was investigated. High-performance liquid chromatography analysis showed that all human fecal samples transformed PhIP but with efficiencies ranging from 1.8 to 96% after 72 h of incubation. Two PhIP-transforming strains, PhIP-M1-a and PhIP-M1-b, were isolated from human feces and identified by fluorescent amplified fragment length polymorphism and pheS sequence analyses as Enterococcus faecium strains. So...
Análisis de especies de Pseudomonas fitopatógenas usando métodos inteligentes de aprendizaje: un ... more Análisis de especies de Pseudomonas fitopatógenas usando métodos inteligentes de aprendizaje: un enfoque general sobre taxonomía y análisis de ácidos grasos dentro del género
BMC Genomics, 2013
Background Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine org... more Background Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus Xanthomonas, and known for its host specificity. As part of a broader pathogenicity study, the genome of a Belgian, virulent Xf strain (LMG 25863) was assembled to draft status and examined for its pathogenicity related gene content. Results The Xf draft genome (4.2 Mb) was considerably smaller than most known Xanthomonas genomes (~5 Mb). Only half of the genes coding for TonB-dependent transporters and cell-wall degrading enzymes that are typically present in other Xanthomonas genomes, were found in Xf. Other missing genes/regions with a possible impact on its plant-host interaction were: i) the three loci for xylan degradation and metabolism, ii) a locus coding for a ß-ketoadipate phenolics catabolism pathway, iii) xcs, one of two Type II Secretion System coding regions in Xant...