Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Soil health indicators and Fusarium wilt suppression in organically managed greenhouse soils
    Bruggen, A.H.C. van; Sharma, K. ; Kaku, E. ; Karfopoulos, S. ; Zelenev, V.V. ; Blok, W.J. - \ 2015
    Applied Soil Ecology 86 (2015). - ISSN 0929-1393 - p. 192 - 201.
    gradient gel-electrophoresis - escherichia-coli o157-h7 - wave-like dynamics - 16s ribosomal-rna - bacterial-populations - microbial-populations - pythium-ultimum - nutrient input - wheat roots - corky root
    Soil health has been associated with internal cycling of nutrients, microbial activity and diversity as well as root disease suppression, which are frequently greater in organically than in conventionally managed soils. Resistance and resilience, measured as amplitude and frequency of oscillations in bacterial communities after a disturbance, were suggested as integral indicators of soil health, but until now there is little proof for this hypothesis. In this study, resistance and resilience of microbial communities and 24 soil chemical and biological parameters were analyzed and correlated to suppression of flax wilt (caused by Fusarium oxysporum f.sp. lini) in three experiments. Soil samples were collected on three different dates from a recently converted organic greenhouse and a similar, neighboring greenhouse under conventional management. The dynamics of copiotrophic and oligotrophic bacteria after a disturbance were monitored, and the resistance and resilience were calculated. The organic soil showed significantly higher water-holding capacity, organic matter content, total C and N contents, C: N ratio of the small particulate organic matter fraction, microbial biomass carbon, oxygen uptake rate, copiotrophic and oligotrophic bacterial communities and suppression of flax wilt incidence. After incorporation of a grass-clover mixture in both soils, the densities of copiotrophic and oligotrophic bacteria oscillated over time. The relative amplitudes of the oscillations (in grass-clover amended over non- amended soil) and the frequencies of the oscillations of both trophic groups were lower for the organic soil, indicating that the resistance and resilience of the microbial community were greater in this soil. These results support the hypothesis that the bacterial response to a disturbance can serve as an integral indicator for soil health, including disease suppressiveness. (C) 2014 Elsevier B.V. All rights reserved.
    Interaction of Collimonas strain IS343 with Rhizoctonia solani at low carbon availability in vitro and in soil
    Senechkin, I.V. ; Overbeek, L.S. van; Er, H.L. ; Vos, O.J. de; Bruggen, A.H.C. van - \ 2013
    European Journal of Plant Pathology 136 (2013)4. - ISSN 0929-1873 - p. 789 - 802.
    organic farming systems - wave-like distributions - bacterial-populations - pythium-ultimum - wheat roots - pseudomonas-fluorescens - microbial-populations - oligotrophic bacteria - conventional soils - disease management
    Collimonas sp. IS343, isolated from an organically-farmed arable soil and characterized as a broad-range oligotrophic bacterium, was shown to degrade chitin and to suppress R. solani mycelium growth under in vitro conditions at high and low carbon availabilities. In contrast to C. fungivorans Ter331, strain IS343 did not respond with an increase in growth rate to higher carbon levels in liquid medium, it reached higher cell numbers in carbon-poor media and it showed better survival in bulk soil. Therefore, it was concluded that strain IS343 cells are better adapted to circumstances of low carbon availability as present in bulk soils than strain Ter331 cells. Further, strain IS343 cells were more suppressive towards R. solani than strain Ter331 cells in vitro. When introduced into soil, strain IS343 cells delayed disease development caused by R. solani AG2-2IIIB in sugar beet plants. These results suggest that strain IS343 cells are able to tentatively suppress R. solani AG2-2IIIB mycelium growth in soil. Potential mechanisms behind the observed suppressive effects can be competition for available nutrients between strain IS343 cells and R. solani mycelium in soil or the production of chitinase as shown for this and other Collimonas species
    Short-term fluctuations of sugar-beet damping-off by Pythium ultimum in relation to changes in bacterial communities after organic amendments to two soils
    He, M. ; Tian, G. ; Semenov, A.M. ; Bruggen, A.H.C. van - \ 2012
    Phytopathology 102 (2012)4. - ISSN 0031-949X - p. 413 - 420.
    gradient gel-electrophoresis - 16s ribosomal-rna - microbial activity - pseudomonas-fluorescens - fertility amendments - rhizoctonia-solani - fungal antagonists - southern blight - wheat roots - populations
    Previously, oscillations in beet seedling damping-off by Pythium ultimum, measured as area under the disease progress curve (AUDPC), were demonstrated after incorporation of organic materials into organic and conventional soils. These periodic fluctuations of P. ultimum infections were cross-correlated with oscillations of copiotrophic CFU at lags of 2 to 4 days. For this article, we investigated whether bacterial communities and microbial activities fluctuated after a disturbance from incorporation of organic materials, and whether these fluctuations were linked to the short-term oscillations in AUDPC of beet seedling damping-off and bacterial populations (CFU) in soil. Soil microbial communities studied by polymerase chain reaction-DGGE analysis of 16S DNA after isolation of total DNA from soil and microbial activities measured as CO2 emission rates were monitored daily for 14 days after addition of grass-clover (GC) or composted manure (CM) into organic versus conventional soils. Similar to our previous findings, AUDPC and density of copiotrophic bacteria oscillated with time. Fluctuations in species richness (S), Shannon diversity index (H), and individual amplicons on DGGE gels were also detected. Oscillations in AUDPC were positively cross-correlated with copiotrophic CFU in all soils. Oscillations in AUDPC were also positively cross-correlated with 19 to 35% of the high-intensity DNA fragments in soils amended with GC but only 2 to 3% of these fragments in CM-amended soils. AUDPC values were negatively cross-correlated with 13 to 17% of the amplicons with low average intensities in CM-amended soils, which were not correlated with densities of copiotrophic CFU. CO2 emission rates had remarkable variations in the initial 7 days after either of the soil amendments but were not associated with daily changes in AUDPC. The results suggest that infection by P. ultimum is hampered by competition from culturable copiotrophic bacteria and some high-intensity DGGE amplicons, because AUDPC is cross-correlated with these variables at lags of 1 to 4 days. However, negative cross-correlations with low-intensity DNA fragments indicate that P. ultimum infection could also be suppressed by antagonistic bacteria with low densities that may be nonculturable species, especially in CM amended soil. The organic soil generally had lower AUDPC values, higher bacterial diversity, and negative cross-correlations between AUDPC and low-intensity DNA fragments (after CM amendment), indicating that specific bacteria that do not attain high densities may contribute to P. ultimum suppression in organic soils
    Daily changes of infections by Pythium ultimum after a nutrient impulse in organic versus conventional soils
    He, M. ; Ma, W. ; Tian, G. ; Blok, W.J. ; Khodzaeva, A. ; Zelenev, V.V. ; Semenov, A.M. ; Bruggen, A.H.C. van - \ 2010
    Phytopathology 100 (2010)6. - ISSN 0031-949X - p. 593 - 600.
    damping-off - bacterial-populations - root-rot - pseudomonas-fluorescens - biological indicators - microbial communities - disease suppression - plant-pathogens - wheat roots - compost
    Bacterial populations (CFU) have been shown to oscillate in wavelike patterns after nutrient impulses in previous studies. The amplitudes and periods of oscillations could possibly be used as indicators of soil health analogous to the stability and resilience of biological populations widely accepted as indicators for ecosystem health. Limited plant and animal disease outbreaks can also be viewed as a manifestation of a healthy soil ecosystem. Two pot experiments were carried out to verify whether damping-off of beet seedlings by Pythium ultimum, measured as area under the disease progress curve (AUDPC), fluctuated over time after incorporation of organic materials into organic versus conventional soils, and to investigate whether daily dynamics of AUDPCs were linked to the dynamics of microbial populations and chemical parameters. AUDPCs oscillated significantly over time when Pythium bioassays were initiated daily after addition of ground grass and clover shoots (GC) into unplanted soils. Similar oscillations with significant harmonics of AUDPC were also observed in composted manure (CM)-amended soils but with smaller amplitudes than in GC-amended soils. The AUDPC harmonics in amended soils had periods similar to those of CFU of copiotrophic bacteria. Cross-correlation analysis demonstrated that periodic fluctuations of P. ultimum infections (AUDPCs) did not coincide with those of copiotrophic CFU but were shifted in phase. It appears that competition or antagonism from some fast-growing bacteria influenced pathogen infections, because these bacterial populations were growing and dying. Soil chemical variables, including pH, dissolved organic carbon, and NO(3)(-)-N, and NH(4)(+)-N contents, changed significantly in the initial 7 days after a nutrient impulse into soils. These changes were cross-correlated with copiotrophic CFU with time lags of approximately 1 to 2 days but were seldom associated with daily changes in AUDPCs. Organically managed soils always had lower AUDPC ratios of amended to nonamended treatments, indicating that organic materials showed stronger suppressive abilities to P. ultimum in organic than in conventional soils. The oscillations in AUDPCs and copiotrophic CFU in amended organic soil also had smaller amplitudes than in amended conventional soil. These results suggested that organically managed soils had a greater resistance and resilience to the disturbance of the amendments and, therefore, could be considered healthier than conventionally managed soils
    Relation between soil health, wave-like fluctuations in microbial populations, and soil-borne plant disease management
    Bruggen, A.H.C. van; Semenov, A.M. ; Diepeningen, A.D. van; Vos, O.J. de; Blok, W.J. - \ 2006
    European Journal of Plant Pathology 115 (2006)1. - ISSN 0929-1873 - p. 105 - 122.
    combining biocontrol agents - organic farming systems - biological-control - bacterial-populations - damping-off - root-rot - species composition - conventional farms - mycorrhizal fungi - wheat roots
    A healthy soil is often defined as a stable soil system with high levels of biological diversity and activity, internal nutrient cycling, and resilience to disturbance. This implies that microbial fluctuations after a disturbance would dampen more quickly in a healthy than in a chronically damaged and biologically impoverished soil. Soil could be disturbed by various processes, for example addition of a nutrient source, tillage, or drying-rewetting. As a result of any disturbance, the numbers of heterotrophic bacteria and of individual species start to oscillate, both in time and space. The oscillations appear as moving waves along the path of a moving nutrient source such as a root tip. The phase and period for different trophic groups and species of bacteria may be shifted indicating that succession occurs. DGGE, Biolog and FAME analysis of subsequent populations in oscillation have confirmed that there is a cyclic succession in microbial communities. Microbial diversity oscillates in opposite direction from oscillations in microbial populations. In a healthy soil, the amplitudes of these oscillations will be small, but the background levels of microbial diversity and activity are high, so that soil-borne diseases will face more competitors and antagonists. However, soil-borne pathogens and antagonists alike will fluctuate in time and space as a result of growing plant roots and other disturbances, and the periods and phases of the oscillations may vary. As a consequence, biological control by members of a single trophic group or species may never be complete, as pathogens will encounter varying populations of the biocontrol agent on the root surface. A mixture of different trophic groups may provide more complete biological control because peaks of different trophic groups occur at subsequent locations along a root. Alternatively, regular addition of soil organic matter may increase background levels of microbial activity, increase nutrient cycling, lower the concentrations of easily available nutrient sources, increase microbial diversity, and enhance natural disease suppression.
    Frequency, diversity and activity of 2,4-diacetylphloroglucinol-producing Pseudomonas spp. in Dutch take-all decline soils
    Souza, J.T. ; Weller, D.M. ; Raaijmakers, J.M. - \ 2003
    Phytopathology 93 (2003)1. - ISSN 0031-949X - p. 54 - 63.
    graminis var tritici - gaeumannomyces-graminis - metabolite 2,4-diacetylphloroglucinol - antibiotic biosynthesis - ecological fitness - biological-control - suppressive soils - wheat roots - rhizosphere - fungus
    Natural suppressiveness of soils to take-all disease of wheat, referred to as take-all decline (TAD), occurs worldwide, It has been postulated that different microbial genera and mechanisms are responsible for TAD in soils from different geographical regions. In growth chamber experiments,,we demonstrated that fluorescent Pseudomonas spp. that produce the antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG) play a key role in the natural suppressiveness of two Dutch TAD soils. First, 2,4-DAPG-producing fluorescent Pseudomonas spp. were present on roots of wheat grown in both of the TAD soils at densities at or above the threshold density required to control take-all of wheat; in a complementary take-all conducive soil, population densities of 2,4-DAPG-producing Pseudomonas spp. were below this threshold level. Second, introduction of 2,4-DAPG-producing strain SSB17, a representative of the dominant geriotypic group found in the Dutch TAD soils, into the take-all conducive soil at population densities similar to the densities, of indigenous 2,4-DAPG producers found in TAD soils provided control of take-all similar to that observed in the TAD soil, Third, a mutant of strain SSB17 deficient in 2,4-DAPG production was not able to control take-all of wheat, indicating that 2,4-DAPG is a key determinant in take-all suppression, These results show that in addition to the physicochemically different TAD soils from Washington State, 2,4-DAPG-producing fluorescent Pseudomonas spp. are also a key component of the natural suppressiveness found in Dutch TAD soils. Furthermore, it is the first time since the initial studies of Gerlagh (1968) that at least part of the mechanisms and microorganisms that operate in Dutch TAD soils are identified. Although quantitatively similar, the genotypic composition of 2,4-DAPG-producing Pseudomonas spp. varied between the Dutch TAD soils and the TAD soils from Washington State.
    Associative Nitrogen Fixation and Root Exudation - What is Theoretically Possible in the Rhizosphere?
    Jones, D.L. ; Farrar, J. ; Giller, K.E. - \ 2003
    Symbiosis 35 (2003)1-3. - ISSN 0334-5114 - p. 19 - 38.
    zea-mays-l - organic-compounds - re-sorption - carbon-flow - amino-acids - wheat roots - soil - transporters - malate - plants
    Root exudation is a key driver of many rhizosphere processes including nitrogen fixation by diazotrophic bacteria residing in the soil. We critically review our knowledge of rhizosphere carbon flow and determine the extent to which rhizodeposition could fuel associative N2 fixation by soil microorganisms. We conclude that most estimates of rhizosphere C flow are fundamentally flawed due to the use of inappropriate methodology combined with a poor mechanistic understanding of root C flow. Using a mathematical model, we predicted that rhizodeposition could under optimal conditions support the fixation of between 0.2 to 4 kg N ha-1 year-1 which is in good agreement with experimentally derived values for natural ecosystems (0.05 to 5 kg N ha-1 y-1). Our model indicated that fixation was highly dependent upon the number of potential N2 fixers in the rhizosphere relative to the total microbial population. If N2 fixer populations could be enhanced, we predict that fixation rates may reach up to 20 kg N ha-1 y-1 given highly optimal conditions which again agree with experimentally derived results. We conclude that whilst the potential for rhizodeposition-driven N2 fixation in the soil is small in comparison to inorganic and symbiotic-N2 fixation inputs, it may be of importance in N-limited ecosystems.
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