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Miro Svercel

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Research Interests: Microbial and soil ecology; plant science; phytopathology; molecular and cell biology and genetics; entomology; interactions between living organisms at different levels and their environment; microbial diversity and physiology; adaptation mechanisms to (extreme) environmental conditions; microbial pathogens and parasites; their mode of actions, evolution and behavior.

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Michele Frapolli

EPFL

Virginia Tech

CSIC (Consejo Superior de Investigaciones Científicas-Spanish National Research Council)

Monika Maurhofer

Swiss Federal Institute of Technology (ETH)

Zurich University of Applied Sciences

Danilo Christen

Swiss Federal Research Station Agroscope

CSIC (Consejo Superior de Investigaciones Científicas-Spanish National Research Council)

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Papers by Miro Svercel

Effect of long-term vineyard monoculture on rhizosphere populations of pseudomonads carrying the antimicrobial biosynthetic genes phlD and/or hcnAB

FEMS Microbiology Ecology, 2009

The impact of repeated culture of perennial plants (i.e. in long-term monoculture) on the ecology... more The impact of repeated culture of perennial plants (i.e. in long-term monoculture) on the ecology of plant-beneficial bacteria is unknown. Here, the influence of extremely long-term monocultures of grapevine (up to 1603 years) on rhizosphere populations of fluorescent pseudomonads carrying the biosynthetic genes phlD for 2,4-diacetylphloroglucinol and/or hcnAB for hydrogen cyanide was determined. Soils from long-term and adjacent short-term monoculture vineyards (or brushland) in four regions of Switzerland were baited with grapevine or tobacco plantlets, and rhizosphere pseudomonads were studied by most probable number (MPN)-PCR. Higher numbers and percentages of phlD 1 and of hcnAB 1 rhizosphere pseudomonads were detected on using soil from long-term vineyards. On focusing on phlD, restriction fragment length polymorphism profiling of the last phlD-positive MPN wells revealed seven phlD alleles (three exclusively on tobacco, thereof two new ones). Higher numbers of phlD alleles coincided with a lower prevalence of the allele displayed by the well-studied biocontrol strain Pseudomonas fluorescens F113. The prevalence of this allele was 35% for tobacco in long-term monoculture soils vs. 4 60% in the other three cases. We conclude that soils from long-term grapevine monocultures represent an untapped resource for isolating novel biocontrol Pseudomonas strains when tobacco is used as bait.

The Influence of Ultraviolet Light on Pathogenicity of Entomopathogenic Fungus Beauveria Bassiana (Balsamo) Vuillemin to the European Corn Borer, Ostrinia Nubilalis Hbn. (Lepidoptera: Crambidae)

The influence of different doses of ultraviolet (UV) light on the pathogenicity of entomopathogen... more The influence of different doses of ultraviolet (UV) light on the pathogenicity of entomopathogenic fungus Beauveria bassiana (Balsamo) Vuillemin to the European corn borer, Ostrinia nubilalis Hbn., and radial growth of fungus was studied in laboratory conditions. The suspensions of B. bassiana isolate SK99 were exposed to UV light. Four different doses of UV light were used in the experiment. The distance between exposed suspensions and UV light source was 0.3 m. Exposure duration was 15, 30, 45 and 60 minutes (as A, B, C and D variants). Control variant SK99 and obtained variants SK99A, SK99B, SK99C and SK99D were cultivated 21 days on Sabourard-dextrose agar. The larvae of O. nubilalis were infected with dry powder consisted of mycelia and spores from fungus cultures. During 10 days, the mortality of infected larvae was evaluated. It was ascertained that UV light exposition significantly influenced the mortality effect of B. bassiana isolates to O. nubilalis larvae. Variant SK99C...

Negative Allelopathy among Cyanobacteria

Cyanobacteria are well known producers of a wide variety of allelochemicals, which positively or ... more Cyanobacteria are well known producers of a wide variety of allelochemicals, which positively or negatively affect sympatric organisms from similar or even different taxons. In the traditional approach for studying allelopathy in water systems, cyanobacteria and photoautotrophic micro-eukaryotes were grouped together under the term of micro-algae. Because these two groups are phylogenetically and phenotypically distinct and the production of allelopathic compounds is often highly species- and even strain-dependent, it is appealing to assess the present available knowledge concerning allelopathy within and among cyanobacteria separately. In this chapter, information is reviewed about i) cyanobacterial production of alleopathic substances, ii) the chemical nature of these allelopathic secondary metabolites, and iii) the mechanisms of the allelopathic inhibition. Furthermore, (iv) the possibility to use allelopathy to control harmful cyanobacterial blooms is discussed.

Use of a Four-Tiered Graph to Parse the Factors Leading to Phenotypic Clustering in Bacteria: A Case Study Based on Samples from the Aletsch Glacier

PLoS ONE, 2013

An understanding of bacterial diversity and evolution in any environment requires knowledge of ph... more An understanding of bacterial diversity and evolution in any environment requires knowledge of phenotypic diversity. In this study, the underlying factors leading to phenotypic clustering were analyzed and interpreted using a novel approach based on a four-tiered graph. Bacterial isolates were organized into equivalence classes based on their phenotypic profile. Likewise, phenotypes were organized in equivalence classes based on the bacteria that manifest them. The linking of these equivalence classes in a four-tiered graph allowed for a quick visual identification of the phenotypic measurements leading to the clustering patterns deduced from principal component analyses. For evaluation of the method, we investigated phenotypic variation in enzyme production and carbon assimilation of members of the genera Pseudomonas and Serratia, isolated from the Aletsch Glacier in Switzerland. The analysis indicates that the genera isolated produce at least six common enzymes and can exploit a wide range of carbon resources, though some specialist species within the pseudomonads were also observed. We further found that pairwise distances between enzyme profiles strongly correlate with distances based on carbon profiles. However, phenotypic distances weakly correlate with phylogenetic distances. The method developed in this study facilitates a more comprehensive understanding of phenotypic clustering than what would be deduced from principal component analysis alone.

Persistence of a biocontrol Pseudomonas inoculant as high populations of culturable and non-culturable cells in 200-cm-deep soil profiles

Soil Biology and Biochemistry, 2012

ABSTRACT Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofe... more ABSTRACT Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofertilization and bioremediation under field conditions. We investigated the persistence and the physiological states of soil-inoculated Pseudomonas protegens (previously Pseudomonas fluorescens) CHAO (10(8) CFU g(-1) surface soil) in different soil microbial habitats in a planted ley (Medicago sativa L.) and an uncovered field plot. At 72 days, colony counts of the inoculant were low in surface soil (uncovered plot) and earthworm guts (ley plot), whereas soil above the plow pan (uncovered plot), and the rhizosphere and worm burrows present until 1.2 m depth (ley plot) were survival hot spots (10(5)-10(6) CFU g(-1), soil). Interestingly, strain CHAO was also detected in the subsoil of both plots, at 10(2)-10(5) CFU g(-1) soil between 1.8 and 2 m depth. However, non-cultured CHAO cells were also evidenced based on immunofluorescence microscopy. Kogure&#39;s direct viable counts of nutrient-responsive cells showed that many more CHAO cells were in a viable but non-culturable (VBNC) or a non-responsive (dormant) state than in a culturable state, and the proportion of cells in those non-cultured states depended on soil microbial habitat. At the most, cells in a VBNC state amounted to 34% (above the plow pan) and those in a dormant state to 89% (in bulk soil between 0.6 and 2 m) of all CHAO cells. The results indicate that field-released Pseudomonas inoculants may persist at high cell numbers, even in deeper soil layers, and display a combination of different physiological states whose prevalence fluctuates according to soil microbial habitats. (C) 2011 Published by Elsevier Ltd.

Distribution of Pseudomonas populations harboring phlD or hcnAB biocontrol genes is related to depth in vineyard soils

Soil Biology and Biochemistry, 2010

The abundance and population structure of pseudomonads in soils collected from long-(1006 years) ... more The abundance and population structure of pseudomonads in soils collected from long-(1006 years) and short-(54 years) term grapevine monocultures in Switzerland were examined across five soil horizons within the 1.20e1.35 m range. Soil samples were baited with grapevine, and rhizosphere pseudomonads containing the biocontrol genes phlD (2,4-diacetylphloroglucinol synthesis) and/or hcnAB (hydrogen cyanide synthesis) were analyzed by MPN-PCR. The numbers of total, phlDþ and hcnABþ pseudomonads decreased with depth by 1.5e2 log (short-term monoculture) and 3e3.5 log (long-term monoculture). In addition, the percentages of phlDþ (except in short-term monoculture) and hcnABþ pseudomonads were also lower in deeper horizons. RFLP-profiling of phlDþ and hcnABþ pseudomonads revealed three phlD and twelve hcnAB alleles overall, but the number of alleles for both decreased in relation to depth. The only phlD allele found in deeper horizons was also found in topsoil, whereas one hcnAB allele (k) found in deeper horizons in long-term monoculture was absent in the topsoil. This suggests that certain Pseudomonas ecotypes are adapted to specific depths. Four hcnAB alleles enabled discrimination between monocultures. We conclude that soil depth is a factor selecting phlD and hcnAB genotypes, and that the allelic diversity of the two biocontrol genes decreases with depth.

Candidatus Syngnamydia Venezia, a Novel Member of the Phylum Chlamydiae from the Broad Nosed Pipefish, Syngnathus typhle

PLoS ONE, 2013

Chlamydia are obligate intracellular bacteria and important pathogens of humans and animals. Chla... more Chlamydia are obligate intracellular bacteria and important pathogens of humans and animals. Chlamydia-related bacteria are also major fish pathogens, infecting epithelial cells of the gills and skin to cause the disease epitheliocystis. Given the wide distribution, ancient origins and spectacular diversity of bony fishes, this group offers a rich resource for the identification and isolation of novel Chlamydia. The broad-nosed pipefish (Syngnathus typhle) is a widely distributed and genetically diverse temperate fish species, susceptible to epitheliocystis across much of its range. We describe here a new bacterial species, Candidatus Syngnamydia venezia; epitheliocystis agent of S. typhle and close relative to other chlamydial pathogens which are known to infect diverse hosts ranging from invertebrates to humans.

Emergent multicellular life cycles in filamentous bacteria owing to density-dependent population dynamics

Journal of The Royal Society Interface, 2011

Filamentous bacteria are the oldest and simplest known multicellular life forms. By using compute... more Filamentous bacteria are the oldest and simplest known multicellular life forms. By using computer simulations and experiments that address cell division in a filamentous context, we investigate some of the ecological factors that can lead to the emergence of a multicellular life cycle in filamentous life forms. The model predicts that if cell division and death rates are dependent on the density of cells in a population, a predictable cycle between short and long filament lengths is produced. During exponential growth, there will be a predominance of multicellular filaments, while at carrying capacity, the population converges to a predominance of short filaments and single cells. Model predictions are experimentally tested and confirmed in cultures of heterotrophic and phototrophic bacterial species. Furthermore, by developing a formulation of generation time in bacterial populations, it is shown that changes in generation time can alter length distributions. The theory predicts t...

PCR amplification of hydrogen cyanide biosynthetic locus hcnAB in Pseudomonas spp

Journal of Microbiological Methods, 2007

A PCR-based assay targeting hcnAB, essential genes for hydrogen cyanide (HCN) biosynthesis, allow... more A PCR-based assay targeting hcnAB, essential genes for hydrogen cyanide (HCN) biosynthesis, allowed sensitive detection of HCN + pseudomonads between logs 2.9 and 3.5 cells per PCR reaction tube. RFLP analysis revealed 13 allele combinations among selected 2,4diacetylphloroglucinol-producing (Phl + )HCN + , and 13 alleles in Phl -HCN + strains from a global collection.

Antagonistic interactions between filamentous heterotrophs and the cyanobacterium Nostoc muscorum

BMC Research Notes, 2011

Background: Little is known about interactions between filamentous heterotrophs and filamentous c... more Background: Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2) and Fibrisoma limi (BUZ 3) with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82) were studied in mixed cultures under nutrient rich (carbon source present in medium) and poor (carbon source absent in medium) conditions. Findings: F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc. The growth and survival of tested heterotrophs was enhanced by the presence of Nostoc or its metabolites, suggesting that the heterotrophs could utilize the autotrophs and its products as a nutrient source. However, the autotroph could withstand and out-compete the heterotrophs under nutrient poor conditions. Conclusions: Our results suggest that the nutrients in cultivation media, which boost or reduce the number of heterotrophs, were the important factor influencing the outcome of the interplay between filamentous heterotrophs and autotrophs. For better understanding of these interactions, additional research is needed. In particular, it is necessary to elucidate the mode of action for lysis by heterotrophs, and the possible defense mechanisms of the autotrophs.

CORRESPONDENCE Open Access

Antagonistic interactions between filamentous heterotrophs and the cyanobacterium Nostoc muscorum

The effect of vineyard long-term monoculture soil on production of volatile compounds and photosynthetic apparatus in grapevine leaves

Vitis, 2010

1) Plant Pathology, Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland 2) Institu... more

Interspecies variation in survival and growth of filamentous heterotrophic bacteria in response to UVC radiation

Journal of Photochemistry and Photobiology B: Biology, 2011

Ultraviolet radiation is an important environmental constraint on the evolution of life. In addit... more Ultraviolet radiation is an important environmental constraint on the evolution of life. In addition to its harmful effects, ultraviolet radiation plays an important role in generating genetic polymorphisms and acting as a selective agent. Understanding how prokaryotes cope with high radiation can give insights on the evolution of life on Earth. Four representative filamentous bacteria from the family Cytophagaceae with different pigmentation were selected and exposed to different doses of UVC radiation (15-32,400 J m À2). The effect of UVC radiation on bacterial survival, growth and morphology were investigated. Results showed high survival in response to UVC for Rudanella lutea and Fibrisoma limi, whereas low survival was observed for Fibrella aestuarina and Spirosoma linguale. S. linguale showed slow growth recovery after ultraviolet exposure, R. lutea and F. limi showed intermediate growth recovery, while F. aestuarina had the fastest recovery among the four tested bacteria. In terms of survival, S. linguale was the most sensitive bacterium whereas R. lutea and F. limi were better at coping with UVC stress. The latter two resumed growth even after 2 h exposure ($10,800 J m À2). Additionally, the ability to form multicellular filaments after exposure was tested using two bacteria: one representative of the high (R. lutea) and one of the low (F. aestuarina) survival rates. The ability to elongate filaments due to cell division was preserved but modified. In R. lutea 10 min exposure reduced the average filament length. The opposite was observed in F. aestuarina, where the 5 and 10 min exposures increased the average filament length. R. lutea and F. limi are potential candidates for further research into survival and resistance to ultraviolet radiation stress.

Four-tiered Graph code v0.2

Four-tiered Graph code v0.2

Long term vineyard monoculture influences the rhizosphere microbial communities

Phytopathologia Mediterranea

BMC Research Notes | Full text | Antagonistic interactions

Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria... more Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2) and Fibrisoma limi (BUZ 3) with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82) were studied in mixed cultures under nutrient rich (carbon source present in medium) and poor (carbon source absent in medium) conditions. Findings: F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc.

BMC Research Notes | Full text | Antagonistic interactions

Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria... more Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2) and Fibrisoma limi (BUZ 3) with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82) were studied in mixed cultures under nutrient rich (carbon source present in medium) and poor (carbon source absent in medium) conditions. Findings: F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc.

Effect of long-term vineyard monoculture on rhizosphere populations of pseudomonads carrying the antimicrobial biosynthetic genes phlD and/or hcnAB

FEMS Microbiology Ecology, 2009

The impact of repeated culture of perennial plants (i.e. in long-term monoculture) on the ecology... more The impact of repeated culture of perennial plants (i.e. in long-term monoculture) on the ecology of plant-beneficial bacteria is unknown. Here, the influence of extremely long-term monocultures of grapevine (up to 1603 years) on rhizosphere populations of fluorescent pseudomonads carrying the biosynthetic genes phlD for 2,4-diacetylphloroglucinol and/or hcnAB for hydrogen cyanide was determined. Soils from long-term and adjacent short-term monoculture vineyards (or brushland) in four regions of Switzerland were baited with grapevine or tobacco plantlets, and rhizosphere pseudomonads were studied by most probable number (MPN)-PCR. Higher numbers and percentages of phlD 1 and of hcnAB 1 rhizosphere pseudomonads were detected on using soil from long-term vineyards. On focusing on phlD, restriction fragment length polymorphism profiling of the last phlD-positive MPN wells revealed seven phlD alleles (three exclusively on tobacco, thereof two new ones). Higher numbers of phlD alleles coincided with a lower prevalence of the allele displayed by the well-studied biocontrol strain Pseudomonas fluorescens F113. The prevalence of this allele was 35% for tobacco in long-term monoculture soils vs. 4 60% in the other three cases. We conclude that soils from long-term grapevine monocultures represent an untapped resource for isolating novel biocontrol Pseudomonas strains when tobacco is used as bait.

The Influence of Ultraviolet Light on Pathogenicity of Entomopathogenic Fungus Beauveria Bassiana (Balsamo) Vuillemin to the European Corn Borer, Ostrinia Nubilalis Hbn. (Lepidoptera: Crambidae)

The influence of different doses of ultraviolet (UV) light on the pathogenicity of entomopathogen... more The influence of different doses of ultraviolet (UV) light on the pathogenicity of entomopathogenic fungus Beauveria bassiana (Balsamo) Vuillemin to the European corn borer, Ostrinia nubilalis Hbn., and radial growth of fungus was studied in laboratory conditions. The suspensions of B. bassiana isolate SK99 were exposed to UV light. Four different doses of UV light were used in the experiment. The distance between exposed suspensions and UV light source was 0.3 m. Exposure duration was 15, 30, 45 and 60 minutes (as A, B, C and D variants). Control variant SK99 and obtained variants SK99A, SK99B, SK99C and SK99D were cultivated 21 days on Sabourard-dextrose agar. The larvae of O. nubilalis were infected with dry powder consisted of mycelia and spores from fungus cultures. During 10 days, the mortality of infected larvae was evaluated. It was ascertained that UV light exposition significantly influenced the mortality effect of B. bassiana isolates to O. nubilalis larvae. Variant SK99C...

Negative Allelopathy among Cyanobacteria

Cyanobacteria are well known producers of a wide variety of allelochemicals, which positively or ... more Cyanobacteria are well known producers of a wide variety of allelochemicals, which positively or negatively affect sympatric organisms from similar or even different taxons. In the traditional approach for studying allelopathy in water systems, cyanobacteria and photoautotrophic micro-eukaryotes were grouped together under the term of micro-algae. Because these two groups are phylogenetically and phenotypically distinct and the production of allelopathic compounds is often highly species- and even strain-dependent, it is appealing to assess the present available knowledge concerning allelopathy within and among cyanobacteria separately. In this chapter, information is reviewed about i) cyanobacterial production of alleopathic substances, ii) the chemical nature of these allelopathic secondary metabolites, and iii) the mechanisms of the allelopathic inhibition. Furthermore, (iv) the possibility to use allelopathy to control harmful cyanobacterial blooms is discussed.

Use of a Four-Tiered Graph to Parse the Factors Leading to Phenotypic Clustering in Bacteria: A Case Study Based on Samples from the Aletsch Glacier

PLoS ONE, 2013

An understanding of bacterial diversity and evolution in any environment requires knowledge of ph... more An understanding of bacterial diversity and evolution in any environment requires knowledge of phenotypic diversity. In this study, the underlying factors leading to phenotypic clustering were analyzed and interpreted using a novel approach based on a four-tiered graph. Bacterial isolates were organized into equivalence classes based on their phenotypic profile. Likewise, phenotypes were organized in equivalence classes based on the bacteria that manifest them. The linking of these equivalence classes in a four-tiered graph allowed for a quick visual identification of the phenotypic measurements leading to the clustering patterns deduced from principal component analyses. For evaluation of the method, we investigated phenotypic variation in enzyme production and carbon assimilation of members of the genera Pseudomonas and Serratia, isolated from the Aletsch Glacier in Switzerland. The analysis indicates that the genera isolated produce at least six common enzymes and can exploit a wide range of carbon resources, though some specialist species within the pseudomonads were also observed. We further found that pairwise distances between enzyme profiles strongly correlate with distances based on carbon profiles. However, phenotypic distances weakly correlate with phylogenetic distances. The method developed in this study facilitates a more comprehensive understanding of phenotypic clustering than what would be deduced from principal component analysis alone.

Persistence of a biocontrol Pseudomonas inoculant as high populations of culturable and non-culturable cells in 200-cm-deep soil profiles

Soil Biology and Biochemistry, 2012

ABSTRACT Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofe... more ABSTRACT Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofertilization and bioremediation under field conditions. We investigated the persistence and the physiological states of soil-inoculated Pseudomonas protegens (previously Pseudomonas fluorescens) CHAO (10(8) CFU g(-1) surface soil) in different soil microbial habitats in a planted ley (Medicago sativa L.) and an uncovered field plot. At 72 days, colony counts of the inoculant were low in surface soil (uncovered plot) and earthworm guts (ley plot), whereas soil above the plow pan (uncovered plot), and the rhizosphere and worm burrows present until 1.2 m depth (ley plot) were survival hot spots (10(5)-10(6) CFU g(-1), soil). Interestingly, strain CHAO was also detected in the subsoil of both plots, at 10(2)-10(5) CFU g(-1) soil between 1.8 and 2 m depth. However, non-cultured CHAO cells were also evidenced based on immunofluorescence microscopy. Kogure&#39;s direct viable counts of nutrient-responsive cells showed that many more CHAO cells were in a viable but non-culturable (VBNC) or a non-responsive (dormant) state than in a culturable state, and the proportion of cells in those non-cultured states depended on soil microbial habitat. At the most, cells in a VBNC state amounted to 34% (above the plow pan) and those in a dormant state to 89% (in bulk soil between 0.6 and 2 m) of all CHAO cells. The results indicate that field-released Pseudomonas inoculants may persist at high cell numbers, even in deeper soil layers, and display a combination of different physiological states whose prevalence fluctuates according to soil microbial habitats. (C) 2011 Published by Elsevier Ltd.

Distribution of Pseudomonas populations harboring phlD or hcnAB biocontrol genes is related to depth in vineyard soils

Soil Biology and Biochemistry, 2010

The abundance and population structure of pseudomonads in soils collected from long-(1006 years) ... more The abundance and population structure of pseudomonads in soils collected from long-(1006 years) and short-(54 years) term grapevine monocultures in Switzerland were examined across five soil horizons within the 1.20e1.35 m range. Soil samples were baited with grapevine, and rhizosphere pseudomonads containing the biocontrol genes phlD (2,4-diacetylphloroglucinol synthesis) and/or hcnAB (hydrogen cyanide synthesis) were analyzed by MPN-PCR. The numbers of total, phlDþ and hcnABþ pseudomonads decreased with depth by 1.5e2 log (short-term monoculture) and 3e3.5 log (long-term monoculture). In addition, the percentages of phlDþ (except in short-term monoculture) and hcnABþ pseudomonads were also lower in deeper horizons. RFLP-profiling of phlDþ and hcnABþ pseudomonads revealed three phlD and twelve hcnAB alleles overall, but the number of alleles for both decreased in relation to depth. The only phlD allele found in deeper horizons was also found in topsoil, whereas one hcnAB allele (k) found in deeper horizons in long-term monoculture was absent in the topsoil. This suggests that certain Pseudomonas ecotypes are adapted to specific depths. Four hcnAB alleles enabled discrimination between monocultures. We conclude that soil depth is a factor selecting phlD and hcnAB genotypes, and that the allelic diversity of the two biocontrol genes decreases with depth.

Candidatus Syngnamydia Venezia, a Novel Member of the Phylum Chlamydiae from the Broad Nosed Pipefish, Syngnathus typhle

PLoS ONE, 2013

Chlamydia are obligate intracellular bacteria and important pathogens of humans and animals. Chla... more Chlamydia are obligate intracellular bacteria and important pathogens of humans and animals. Chlamydia-related bacteria are also major fish pathogens, infecting epithelial cells of the gills and skin to cause the disease epitheliocystis. Given the wide distribution, ancient origins and spectacular diversity of bony fishes, this group offers a rich resource for the identification and isolation of novel Chlamydia. The broad-nosed pipefish (Syngnathus typhle) is a widely distributed and genetically diverse temperate fish species, susceptible to epitheliocystis across much of its range. We describe here a new bacterial species, Candidatus Syngnamydia venezia; epitheliocystis agent of S. typhle and close relative to other chlamydial pathogens which are known to infect diverse hosts ranging from invertebrates to humans.

Emergent multicellular life cycles in filamentous bacteria owing to density-dependent population dynamics

Journal of The Royal Society Interface, 2011

Filamentous bacteria are the oldest and simplest known multicellular life forms. By using compute... more Filamentous bacteria are the oldest and simplest known multicellular life forms. By using computer simulations and experiments that address cell division in a filamentous context, we investigate some of the ecological factors that can lead to the emergence of a multicellular life cycle in filamentous life forms. The model predicts that if cell division and death rates are dependent on the density of cells in a population, a predictable cycle between short and long filament lengths is produced. During exponential growth, there will be a predominance of multicellular filaments, while at carrying capacity, the population converges to a predominance of short filaments and single cells. Model predictions are experimentally tested and confirmed in cultures of heterotrophic and phototrophic bacterial species. Furthermore, by developing a formulation of generation time in bacterial populations, it is shown that changes in generation time can alter length distributions. The theory predicts t...

PCR amplification of hydrogen cyanide biosynthetic locus hcnAB in Pseudomonas spp

Journal of Microbiological Methods, 2007

A PCR-based assay targeting hcnAB, essential genes for hydrogen cyanide (HCN) biosynthesis, allow... more A PCR-based assay targeting hcnAB, essential genes for hydrogen cyanide (HCN) biosynthesis, allowed sensitive detection of HCN + pseudomonads between logs 2.9 and 3.5 cells per PCR reaction tube. RFLP analysis revealed 13 allele combinations among selected 2,4diacetylphloroglucinol-producing (Phl + )HCN + , and 13 alleles in Phl -HCN + strains from a global collection.

Antagonistic interactions between filamentous heterotrophs and the cyanobacterium Nostoc muscorum

BMC Research Notes, 2011

Background: Little is known about interactions between filamentous heterotrophs and filamentous c... more Background: Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2) and Fibrisoma limi (BUZ 3) with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82) were studied in mixed cultures under nutrient rich (carbon source present in medium) and poor (carbon source absent in medium) conditions. Findings: F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc. The growth and survival of tested heterotrophs was enhanced by the presence of Nostoc or its metabolites, suggesting that the heterotrophs could utilize the autotrophs and its products as a nutrient source. However, the autotroph could withstand and out-compete the heterotrophs under nutrient poor conditions. Conclusions: Our results suggest that the nutrients in cultivation media, which boost or reduce the number of heterotrophs, were the important factor influencing the outcome of the interplay between filamentous heterotrophs and autotrophs. For better understanding of these interactions, additional research is needed. In particular, it is necessary to elucidate the mode of action for lysis by heterotrophs, and the possible defense mechanisms of the autotrophs.

CORRESPONDENCE Open Access

Antagonistic interactions between filamentous heterotrophs and the cyanobacterium Nostoc muscorum

The effect of vineyard long-term monoculture soil on production of volatile compounds and photosynthetic apparatus in grapevine leaves

Vitis, 2010

1) Plant Pathology, Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland 2) Institu... more

Interspecies variation in survival and growth of filamentous heterotrophic bacteria in response to UVC radiation

Journal of Photochemistry and Photobiology B: Biology, 2011

Ultraviolet radiation is an important environmental constraint on the evolution of life. In addit... more Ultraviolet radiation is an important environmental constraint on the evolution of life. In addition to its harmful effects, ultraviolet radiation plays an important role in generating genetic polymorphisms and acting as a selective agent. Understanding how prokaryotes cope with high radiation can give insights on the evolution of life on Earth. Four representative filamentous bacteria from the family Cytophagaceae with different pigmentation were selected and exposed to different doses of UVC radiation (15-32,400 J m À2). The effect of UVC radiation on bacterial survival, growth and morphology were investigated. Results showed high survival in response to UVC for Rudanella lutea and Fibrisoma limi, whereas low survival was observed for Fibrella aestuarina and Spirosoma linguale. S. linguale showed slow growth recovery after ultraviolet exposure, R. lutea and F. limi showed intermediate growth recovery, while F. aestuarina had the fastest recovery among the four tested bacteria. In terms of survival, S. linguale was the most sensitive bacterium whereas R. lutea and F. limi were better at coping with UVC stress. The latter two resumed growth even after 2 h exposure ($10,800 J m À2). Additionally, the ability to form multicellular filaments after exposure was tested using two bacteria: one representative of the high (R. lutea) and one of the low (F. aestuarina) survival rates. The ability to elongate filaments due to cell division was preserved but modified. In R. lutea 10 min exposure reduced the average filament length. The opposite was observed in F. aestuarina, where the 5 and 10 min exposures increased the average filament length. R. lutea and F. limi are potential candidates for further research into survival and resistance to ultraviolet radiation stress.

Four-tiered Graph code v0.2

Four-tiered Graph code v0.2

Long term vineyard monoculture influences the rhizosphere microbial communities

Phytopathologia Mediterranea

BMC Research Notes | Full text | Antagonistic interactions

Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria... more Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2) and Fibrisoma limi (BUZ 3) with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82) were studied in mixed cultures under nutrient rich (carbon source present in medium) and poor (carbon source absent in medium) conditions. Findings: F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc.

BMC Research Notes | Full text | Antagonistic interactions

Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria... more Little is known about interactions between filamentous heterotrophs and filamentous cyanobacteria. Here, interactions between the filamentous heterotrophic bacteria Fibrella aestuarina (strain BUZ 2) and Fibrisoma limi (BUZ 3) with an axenic strain of the autotrophic filamentous cyanobacterium Nostoc muscorum (SAG 25.82) were studied in mixed cultures under nutrient rich (carbon source present in medium) and poor (carbon source absent in medium) conditions. Findings: F. aestuarina BUZ 2 significantly reduced the cyanobacterial population whereas F. limi BUZ 3 did not. Physical contact between heterotrophs and autotroph was observed and the cyanobacterial cells showed some level of damage and lysis. Therefore, either contact lysis or entrapment with production of extracellular compounds in close vicinity of host cells could be considered as potential modes of action. The supernatants from pure heterotrophic cultures did not have an effect on Nostoc cultures. However, supernatant from mixed cultures of BUZ 2 and Nostoc had a negative effect on cyanobacterial growth, indicating that the lytic compounds were only produced in the presence of Nostoc.

Negative Allelopathy among Cyanobacteria

Cyanobacteria: Ecology, Toxicology and Management, May 2013

Cyanobacteria are well known producers of a wide variety of allelochemicals, which positively or ... more Cyanobacteria are well known producers of a wide variety of allelochemicals, which positively or negatively affect sympatric organisms from similar or even different taxons. In the traditional approach for studying allelopathy in water systems, cyanobacteria and photoautotrophic micro-eukaryotes were grouped together under the term of micro-algae. Because these two groups are phylogenetically and phenotypically distinct and the production of allelopathic compounds is often highly species- and even strain-dependent, it is appealing to assess the present available knowledge concerning allelopathy within and among cyanobacteria separately.
In this chapter, information is reviewed about i) cyanobacterial production of alleopathic substances, ii) the chemical nature of these allelopathic secondary metabolites, and iii) the mechanisms of the allelopathic inhibition. Furthermore, (iv) the possibility to use allelopathy to control harmful cyanobacterial blooms is discussed.