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.

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Soil fauna diversity increases CO2 but suppresses N2O emissions from soil
Lubbers, Ingrid M. ; Berg, Matty P. ; Deyn, Gerlinde B. De; Putten, Wim H. van der; Groenigen, Jan Willem van - \ 2019
Global Change Biology (2019). - ISSN 1354-1013
community composition - functional dissimilarity - GHG mitigation - net diversity effect - soil-derived GHG emission - species richness

Soil faunal activity can be a major control of greenhouse gas (GHG) emissions from soil. Effects of single faunal species, genera or families have been investigated, but it is unknown how soil fauna diversity may influence emissions of both carbon dioxide (CO2, end product of decomposition of organic matter) and nitrous oxide (N2O, an intermediate product of N transformation processes, in particular denitrification). Here, we studied how CO2 and N2O emissions are affected by species and species mixtures of up to eight species of detritivorous/fungivorous soil fauna from four different taxonomic groups (earthworms, potworms, mites, springtails) using a microcosm set-up. We found that higher species richness and increased functional dissimilarity of species mixtures led to increased faunal-induced CO2 emission (up to 10%), but decreased N2O emission (up to 62%). Large ecosystem engineers such as earthworms were key drivers of both CO2 and N2O emissions. Interestingly, increased biodiversity of other soil fauna in the presence of earthworms decreased faunal-induced N2O emission despite enhanced C cycling. We conclude that higher soil fauna functional diversity enhanced the intensity of belowground processes, leading to more complete litter decomposition and increased CO2 emission, but concurrently also resulting in more complete denitrification and reduced N2O emission. Our results suggest that increased soil fauna species diversity has the potential to mitigate emissions of N2O from soil ecosystems. Given the loss of soil biodiversity in managed soils, our findings call for adoption of management practices that enhance soil biodiversity and stimulate a functionally diverse faunal community to reduce N2O emissions from managed soils.

Data from: Cross-seasonal legacy effects of arthropod community on plant fitness in perennial plants
Stam, J.M. ; Kos, M. ; Dicke, M. ; Poelman, E.H. - \ 2019
Plant–herbivore interactions - community composition - community dynamics - log term effects - seed set - insect-plant interactions - priority effect - Brassica oleracea
1. In perennial plants, interactions with other community members during the vegetative growth phase may influence community assembly during subsequent reproductive years and may influence plant fitness. It is well known that plant responses to herbivory affect community assembly within a growing season, but whether plant-herbivore interactions result in legacy effects on community assembly across seasons has received little attention. Moreover, whether plant-herbivore interactions during the vegetative growing season are important in predicting plant fitness directly or indirectly through legacy effects is poorly understood. 2. Here, we tested whether plant-arthropod interactions in the vegetative growing season of perennial wild cabbage plants, Brassica oleracea, result in legacy effects in arthropod community assembly in the subsequent reproductive season and whether legacy effects have plant fitness consequences. We monitored the arthropod community on plants that had been induced with either aphids, caterpillars or no herbivores in a full-factorial design across two years. We quantified the plant traits ‘height’, ‘number of leaves’ and ‘number of flowers’ to understand mechanisms that may mediate legacy effects. We measured seed production in the second year to evaluate plant fitness consequences of legacy effects. 3. Although we did not find community responses to the herbivory treatments, our data show that community composition in one year leaves a legacy on community composition in a second year: predator community composition co-varied across years. Structural Equation Modelling analyses indicated that herbivore communities in the vegetative year correlated with plant performance traits that may have caused a legacy effect on especially predator community assembly in the subsequent reproductive year. Interestingly, the legacy of the herbivore community in the vegetative year predicted plant fitness better than the herbivore community that directly interacted with plants in the reproductive year. 4. Synthesis Thus, legacy effects of plant-herbivore interactions affect community assembly on perennial plants across growth seasons and these processes may affect plant reproductive success. We argue that plant-herbivore interactions in the vegetative phase as well as cross seasonal legacy effects caused by plant responses to arthropod herbivory may be important in perennial plant trait evolution such as ontogenetic variation in growth and defence strategies.
Contrasting effects of host species and phylogenetic diversity on the occurrence of HPAI H5N1 in European wild birds
Huang, Zheng Y.X. ; Xu, Chi ; Langevelde, Frank van; Ma, Yuying ; Langendoen, Tom ; Mundkur, Taej ; Si, Yali ; Tian, Huaiyu ; Kraus, Robert H.S. ; Gilbert, Marius ; Han, Guan Zhu ; Ji, Xiang ; Prins, Herbert H.T. ; Boer, Willem F. de - \ 2019
Journal of Animal Ecology 88 (2019)7. - ISSN 0021-8790 - p. 1044 - 1053.
avian influenza - community composition - dilution effect - diversity–disease relationship - phylogenetic distance - waterfowl

Studies on the highly pathogenic avian influenza (HPAI) H5N1 suggest that wild bird migration may facilitate its long-distance spread, yet the role of wild bird community composition in its transmission risk remains poorly understood. Furthermore, most studies on the diversity–disease relationship focused on host species diversity without considering hosts’ phylogenetic relationships, which may lead to rejecting a species diversity effect when the community has host species that are only distantly related. Here, we explored the influence of waterbird community composition for determining HPAI H5N1 occurrence in wild birds in a continental-scale study across Europe. In particular, we tested the diversity–disease relationship using both host species diversity and host phylogenetic diversity. Our results provide the first demonstration that host community composition—compared with previously identified environmental risk factors—can also effectively explain the spatial pattern of H5N1 occurrence in wild birds. We further show that communities with more higher risk host species and more closely related species have a higher risk of H5N1 outbreaks. Thus, both host species diversity and community phylogenetic structure, in addition to environmental factors, jointly influence H5N1 occurrence. Our work not only extends the current theory on the diversity–disease relationship, but also has important implications for future monitoring of H5N1 and other HPAI subtypes.

Traditional plant functional groups explain variation in economic but not size-related traits across the tundra biome
Thomas, H.J.D. ; Myers-Smith, I.H. ; Bjorkman, A.D. ; Elmendorf, S.C. ; Blok, D. ; Cornelissen, J.H.C. ; Forbes, B.C. ; Hollister, R.D. ; Normand, S. ; Prevéy, J.S. ; Rixen, C. ; Schaepman-Strub, G. ; Wilmking, M. ; Wipf, S. ; Cornwell, W. ; Kattge, J. ; Goetz, S.J. ; Guay, K.C. ; Alatalo, J.M. ; Anadon-Rosell, A. ; Angers-Blondin, S. ; Berner, L.T. ; Björk, R.G. ; Buchwal, A. ; Buras, A. ; Carbognani, M. ; Christie, K. ; Siegwart Collier, L. ; Cooper, E.J. ; Eskelinen, A. ; Frei, E.R. ; Grau, O. ; Grogan, P. ; Hallinger, M. ; Heijman, M.M.P.D. ; Hermanutz, L. ; Hudson, J.M.G. ; Hülber, K. ; Iturrate-Garcia, M. ; Iversen, C.M. ; Jaroszynska, F. ; Johnstone, J.F. ; Kaarlejärvi, E. ; Kulonen, A. ; Lamarque, L.J. ; Lévesque, E. ; Beest, M. Te; Vries, F.T. de; Ozinga, W.A. ; Bodegom, P.M. van - \ 2018
Global Ecology and Biogeography (2018). - ISSN 1466-822X
cluster analysis - community composition - ecosystem function - plant functional groups - plant functional types - plant traits - tundra biome - vegetation change

Aim: Plant functional groups are widely used in community ecology and earth system modelling to describe trait variation within and across plant communities. However, this approach rests on the assumption that functional groups explain a large proportion of trait variation among species. We test whether four commonly used plant functional groups represent variation in six ecologically important plant traits. Location: Tundra biome. Time period: Data collected between 1964 and 2016. Major taxa studied: 295 tundra vascular plant species. Methods: We compiled a database of six plant traits (plant height, leaf area, specific leaf area, leaf dry matter content, leaf nitrogen, seed mass) for tundra species. We examined the variation in species-level trait expression explained by four traditional functional groups (evergreen shrubs, deciduous shrubs, graminoids, forbs), and whether variation explained was dependent upon the traits included in analysis. We further compared the explanatory power and species composition of functional groups to alternative classifications generated using post hoc clustering of species-level traits. Results: Traditional functional groups explained significant differences in trait expression, particularly amongst traits associated with resource economics, which were consistent across sites and at the biome scale. However, functional groups explained 19% of overall trait variation and poorly represented differences in traits associated with plant size. Post hoc classification of species did not correspond well with traditional functional groups, and explained twice as much variation in species-level trait expression. Main conclusions: Traditional functional groups only coarsely represent variation in well-measured traits within tundra plant communities, and better explain resource economic traits than size-related traits. We recommend caution when using functional group approaches to predict tundra ecosystem change, or ecosystem functions relating to plant size, such as albedo or carbon storage. We argue that alternative classifications or direct use of specific plant traits could provide new insight into ecological prediction and modelling.

Where, when and how plant–soil feedback matters in a changing world
Putten, Wim H. van der; Bradford, Mark A. ; Brinkman, E.P. ; Voorde, Tess F.J. van de; Veen, G.F. - \ 2016
Functional Ecology 30 (2016). - ISSN 0269-8463 - p. 1109 - 1121.
biodiversity loss - carbon and nutrient cycling - climate change - community composition - invasive plants - land use - plant–soil feedback triangle - range expansion

It is increasingly acknowledged that plant–soil feedbacks may play an important role in driving the composition of plant communities and functioning of terrestrial ecosystems. However, the mechanistic understanding of plant–soil feedbacks, as well as their roles in natural ecosystems in proportion to other possible drivers, is still in its infancy. Such knowledge will enhance our capacity to determine the contribution of plant–soil feedback to community and ecosystem responses under global environmental change. Here, we review how plant–soil feedbacks may develop under extreme drought and precipitation events, CO2 and nitrogen enrichment, temperature increase, land use change and plant species loss vs. gain. We present a framework for opening the ‘black box of soil’ considering the responses of the various biotic components (enemies, symbionts and decomposers) of plant–soil feedback to the global environmental changes, and we discuss how to integrate these components to understand and predict the net effects of plant–soil feedbacks under the various scenarios of change. To gain an understanding of how plant–soil feedback plays out in realistic settings, we also use the framework to discuss its interaction with other drivers of plant community composition, including competition, facilitation, herbivory, and soil physical and chemical properties. We conclude that understanding the role that plant–soil feedback plays in shaping the responses of plant community composition and ecosystem processes to global environmental changes requires unravelling the individual contributions of enemies, symbionts and decomposers. These biotic factors may show different response rates and strengths, thereby resulting in different net magnitudes and directions of plant–soil feedbacks under various scenarios of global change. We also need tests of plant–soil feedback under more realistic conditions to determine its contribution to changes in patterns and processes in the field, both at ecologically and evolutionary relevant time-scales.

Species-specific plant-soil feedback effects on above-ground plant-insect interactions
Kos, M. ; Tuijl, M.A.B. ; Roo, J. de; Mulder, P.P.J. ; Bezemer, T.M. - \ 2015
Journal of Ecology 103 (2015)4. - ISSN 0022-0477 - p. 904 - 914.
below-ground herbivory - pyrrolizidine alkaloids - senecio-jacobaea - multitrophic interactions - community composition - tyria-jacobaeae - responses - succession - pathogens - nutrients
1.Plant–soil feedback (PSF) effects on plant performance strongly depend on the plant species that conditioned the soil. Recent studies have shown that PSF can change above-ground plant–insect interactions via soil-mediated changes in plant quality, but whether these effects depend on species-specific soil conditioning is unknown. We examined how PSF effects of several plant species influence above-ground plant–aphid interactions. 2.We grew ragwort (Jacobaea vulgaris) in field soil conditioned specifically by 10 plant species, belonging to three functional groups (grasses, forbs and legumes), in a multispecies mixture of the conditioned soils and in control (unconditioned) field soil. We measured plant biomass, concentrations of primary (amino acids) and secondary (pyrrolizidine alkaloids) metabolites in phloem exudates, and performance of the generalist aphid Brachycaudus cardui and the specialist Aphis jacobaeae. 3.We observed that plant species, via species-specific effects on soil fungal communities, exerted unique plant–soil effects on J. vulgaris biomass, amino acid concentrations in phloem exudates and aphid performance. The direction and magnitude of the species-specific PSF effects on aphid performance differed between both aphid species. PSF effects on soil fungal communities, plant biomass and A. jacobaeae performance also differed between grasses, forbs and legumes, with soil conditioning by forbs resulting in lowest plant biomass and aphid performance. 4.Synthesis. Our study provides novel evidence that PSF effects on above-ground plant–insect interactions are highly species specific. Our results add a new dimension to the rapidly developing research fields of PSF and above-below-ground interactions, and highlights that these fields are tightly linked.
Plant-soil feedback effects on plant quality and performance of an aboveground herbivore interact with fertilisation
Kos, M. ; Maarten, A. ; Tuijl, M.A.B. ; Roo, J. de; Mulder, P.P.J. ; Bezemer, T.M. - \ 2015
Oikos 124 (2015)5. - ISSN 0030-1299 - p. 658 - 667.
below-ground herbivory - pyrrolizidine alkaloids - senecio-jacobaea - tyria-jacobaeae - multitrophic interactions - nitrate fertilization - community composition - insect community - aphid - pathogens
Plant–soil feedback (PSF) effects on plant performance can be influenced by the availability of nutrients in the soil. Recent studies have shown that PSF effects can also change aboveground plant–insect interactions via soil-mediated changes in plant quality, but whether this is influenced by soil nutrient availability is unknown. We examined how fertilisation influences PSF effects on aboveground plant-aphid interactions in ragwort Jacobaea vulgaris. We grew J. vulgaris in soil conditioned by conspecific plants and in unconditioned soil at two levels of fertilisation and measured soil fungal communities, plant biomass, concentrations of primary (amino acids) and secondary (pyrrolizidine alkaloids; PAs) metabolites in phloem exudates, performance of the specialist aphid Aphis jacobaeae and sequestration of PAs by the aphid. We observed a strong interaction between soil conditioning and fertilisation on amino acid and PA concentrations in phloem exudates of J. vulgaris and on aphid performance, with opposite effects of soil conditioning at the two fertilisation levels. Plant biomass was reduced by soil conditioning and increased by fertilisation. Aphids contained high PA concentrations, converted N-oxides into tertiary amines and preferentially sequestered certain PA compounds, but PA sequestration was not affected by any of the treatments. We conclude that effects of PSF and fertilisation on plant chemistry and aphid performance are interdependent. Our study highlights the need to consider the importance of abiotic soil conditions on the outcome of PSF effects on aboveground plant–insect interactions.
Volatiles produced by the mycophagous soil bacterium Collimonas
Garbeva, P. ; Hordijk, C. ; Gerards, S. ; Boer, W. de - \ 2014
FEMS microbiology ecology 87 (2014)3. - ISSN 0168-6496 - p. 639 - 649.
community composition - organic-compounds - genus collimonas - fungal hyphae - bulk soil - sp nov. - growth - fungivorans - rhizosphere - fungistasis
It is increasingly recognized that volatile organic compounds play an import role during interactions between soil microorganisms. Here, we examined the possible involvement of volatiles in the interaction of Collimonas bacteria with soil fungi. The genus Collimonas is known for its ability to grow at the expense of living fungi (mycophagy), and antifungal volatiles may contribute to the attack of fungi by these bacteria. We analyzed the composition of volatiles produced by Collimonas on agar under different nutrient conditions and studied the effect on fungal growth. The volatiles had a negative effect on the growth of a broad spectrum of fungal species. Collimonas bacteria did also produce volatiles in sand microcosms supplied with artificial root exudates. The production of volatiles in sand microcosms was enhanced by the presence of fungi. The overall picture that we get from our study is that antifungal volatiles produced by Collimonas could play an important role in realizing its mycophagous lifestyle. The current work is also interesting for understanding the ecological relevance of volatile production by soil bacteria in general as we found strong influences of root exudates composition and incubation conditions on the spectrum of volatiles produced.
Impact of interspecific interactions on antimicrobial activity among soil bacteria
Tyc, O. ; Berg, M. van den; Gerards, S. ; Veen, J.A. van; Raaijmakers, J.M. ; Boer, W. de; Garbeva, P. - \ 2014
Frontiers in Microbiology 5 (2014). - ISSN 1664-302X
community composition - bacillus-subtilis - gene-expression - antibiotics - diversity - rhizosphere - inhibition - environment - resistance - reveals
Certain bacterial species produce antimicrobial compounds only in the presence of a competing species. However, little is known on the frequency of interaction-mediated induction of antibiotic compound production in natural communities of soil bacteria. Here we developed a high-throughput method to screen for the production of antimicrobial activity by monocultures and pair-wise combinations of 146 phylogenetically different bacteria isolated from similar soil habitats. Growth responses of two human pathogenic model organisms, Escherichia coli WA321 and Staphylococcus aureus 533R4, were used to monitor antimicrobial activity. From all isolates, 33% showed antimicrobial activity only in monoculture and 42% showed activity only when tested in interactions. More bacterial isolates were active against S. aureus than against E. coli. The frequency of interaction-mediated induction of antimicrobial activity was 6% (154 interactions out of 2798) indicating that only a limited set of species combinations showed such activity. The screening revealed also interaction-mediated suppression of antimicrobial activity for 22% of all combinations tested. Whereas all patterns of antimicrobial activity (non-induced production, induced production and suppression) were seen for various bacterial classes, interaction-mediated induction of antimicrobial activity was more frequent for combinations of Flavobacteria and alpha- Proteobacteria. The results of our study give a first indication on the frequency of interference competitive interactions in natural soil bacterial communities which may forms a basis for selection of bacterial groups that are promising for the discovery of novel, cryptic antibiotics.
Determination of potential N2O-reductase activity in soil
Qin, S.P. ; Yuan, H.J. ; Hu, C.S. ; Oenema, O. ; Zhang, Y.M. ; Li, X.X. - \ 2014
Soil Biology and Biochemistry 70 (2014). - ISSN 0038-0717 - p. 205 - 210.
nitrous-oxide reduction - acetylene inhibition technique - denitrifying bacteria - community composition - pseudomonas-mandelii - aquatic sediments - marine-sediments - enzyme-activity - n2o reduction - denitrification
Determination of N2O-reductase activity in soil is important for understanding the microbial regulation of nitrous oxide (N2O) concentrations in soil. Unfortunately, there are no easily applicable and accurate methods for determining N2O-reductase activity, which frustrates the understanding of the mechanisms that control soil management effects on denitrification and N2O emissions. The objectives of the study reported here were (i) to define the optimal experimental conditions for the determination of potential N2O-reductase activity in soil, (ii) to compare the direct-N-2 method with the acetylene inhibition technique, and (iii) to investigate the effects of long-term nitrogen (N) fertilization on the potential N2O-reductase activity. Various substrate concentrations, water/soil ratios, incubation times, temperatures and pH values were tested to find the optimal conditions for the potential N2O-reductase activity in soils from two sites. Then, the potential N2O-reductase activity was determined under optimal conditions (10 g soil, 10 ml buffer solution, pH 9, 40 degrees C, 100 ppmv N2O) in soils from the long-term N fertilization experiment. There were significant differences between soils in potential N2O-reductase activity, but the optimal experimental conditions were similar. The acetylene inhibition technique underestimated N2O-reductase activity in soil relative to the direct-N-2 method, especially in the treatment where fertilizer N was withheld for 15 yrs. We recommend that the optimal experimental conditions for the determination of the potential N2O-reductase activity are established also for other soils. More studies are needed to fully understand the interactive effects of long-term N fertilization on nosZ gene expression and N2O-reductase activity in soils. (C) 2014 Elsevier Ltd. All rights reserved.
Assessing effects of the fungicide tebuconazole to heterotrophic microbes in aquatic microcosms
Dimitrov, M.R. ; Kosol, Sujitra ; Smidt, H. ; Brink, P.J. van den; Wijngaarden, R.P.A. van; Brock, T.C.M. ; Maltby, L. - \ 2014
Science of the Total Environment 490 (2014). - ISSN 0048-9697 - p. 1002 - 1011.
gradient gel-electrophoresis - leaf-litter decomposition - fresh-water microcosms - coal-mine effluent - decaying leaves - gammarus-pulex - community composition - fungal communities - primary producers - stream fungi
Aquatic ecological risk assessment of fungicides in Europe under Regulation 1107/2009/EC does not currently assess risk to non-target bacteria and fungi. Rather, regulatory acceptable concentrations based on ecotoxicological data obtained from studies with fish, invertebrates and primary producers (including algae) are assumed to be protective to all other aquatic organisms. Here we explore the validity of this assumption by investigating the effects of a fungicide (tebuconazole) applied at its "non-microbial" HC5 concentration (the concentration that is hazardous to 5% of the tested taxa) and derived from acute single species toxicity tests on fish, invertebrates and primary producers (including algae) on the community structure and functioning of heterotrophic microbes (bacteria and aquatic fungi) in a semi-field study, using novel molecular techniques. In our study, a treatment-related effect of tebuconazole (238 µg/L) on either fungal biomass associated with leaf material or leaf decomposition or the composition of the fungal community associated with sediment could not be demonstrated. Moreover, treatment-related effects on bacterial communities associated with sediment and leaf material were not detected. However, tebuconazole exposure did significantly reduce conidia production and altered fungal community composition associated with leaf material. An effect on a higher trophic level was observed when Gammarus pulex were fed tebuconazole-exposed leaves, which caused a significant decrease in their feeding rate. Therefore, tebuconazole may affect aquatic fungi and fungally mediated processes even when applied at its "non-microbial" HC5 concentration.
Impact of organic carbon and nutrients mobilized during chemical oxidation on subsequent bioremediation of a diesel-contaminated soil
Sutton, N.B. ; Grotenhuis, J.T.C. ; Rijnaarts, H.H.M. - \ 2014
Chemosphere 97 (2014). - ISSN 0045-6535 - p. 64 - 70.
in-situ ozonation - community composition - matter - biodegradation - oil - bioavailability - oxidants - sorption
Remediation with in situ chemical oxidation (ISCO) impacts soil organic matter (SOM) and the microbial community, with deleterious effects on the latter being a major hurdle to coupling ISCO with in situ bioremediation (ISB). We investigate treatment of a diesel-contaminated soil with Fenton’s reagent and modified Fenton’s reagent coupled with a subsequent bioremediation phase of 187 d, both with and without nutrient amendment. Chemical oxidation mobilized SOM into the liquid phase, producing dissolved organic carbon (DOC) concentrations 8–16 times higher than the untreated field sample. Higher aqueous concentrations of nitrogen and phosphorous species were also observed following oxidation; increased 14–172 times. During the bioremediation phase, dissolved carbon and nutrient species were utilized for microbial growth-yielding DOC concentrations similar to field sample levels within 56 d of incubation. In the absence of nutrient amendment, the highest microbial respiration rates were correlated with higher availability of nitrogen and phosphorus species mobilized by oxidation. Significant diesel degradation was only observed following nutrient amendment, implying that nutrients mobilized by chemical oxidation can increase microbial activity but are insufficient for bioremediation. While all bioremediation occurred in the first 28 d of incubation in the biotic control microcosm with nutrient amendment, biodegradation continued throughout 187 d of incubation following chemical oxidation, suggesting that chemical treatment also affects the desorption of organic contaminants from SOM. Overall, results indicate that biodegradation of DOC, as an alternative substrate to diesel, and biological utilization of mobilized nutrients have implications for the success of coupled ISCO and ISB treatments.
Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils
Sutton, N.B. ; Langenhoff, A.A.M. ; Hidalgo Lasso, D. ; Zaan, B.M. van der; Gaans, P. van; Maphosa, F. ; Smidt, H. ; Grotenhuis, J.T.C. ; Rijnaarts, H.H.M. - \ 2014
Applied Microbiology and Biotechnology 98 (2014)6. - ISSN 0175-7598 - p. 2751 - 2764.
polycyclic aromatic-hydrocarbons - gradient gel-electrophoresis - in-situ ozonation - real-time pcr - crude-oil - fentons reagent - biological remediation - community composition - organic-matter - ribosomal-rna
To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1–2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.
Soil inoculation method determines the strength of plant-soil interactions
Voorde, T.F.J. van de; Ruijten, M. ; Putten, W.H. van der; Bezemer, T.M. - \ 2012
Soil Biology and Biochemistry 55 (2012). - ISSN 0038-0717 - p. 1 - 6.
vesicular-arbuscular mycorrhizal - senecio-jacobaea - community composition - feedback - biota - microorganisms - rhizosphere - succession - diversity - dynamics
There is increasing evidence that interactions between plants and biotic components of the soil influence plant productivity and plant community composition. Many plant–soil feedback experiments start from inoculating relatively small amounts of natural soil to sterilized bulk soil. These soil inocula may include a variety of size classes of soil biota, each having a different role in the observed soil feedback effects. In order to examine what may be the effect of various size classes of soil biota we compared inoculation with natural field soil sieved through a 1 mm mesh, a soil suspension also sieved through a 1 mm mesh, and a microbial suspension sieved through a 20 µm mesh. We tested these effects for different populations of the same plant species and for different soil origins. Plant biomass was greatest in pots inoculated with the microbial suspension and smallest in pots inoculated with sieved soil, both in the first and second growth phase, and there was no significant population or soil origin effect. Plant-feeding nematodes were almost exclusively found in the sieved soil treatment. We show that processing the soil to obtain a microbial suspension reduces the strength of the soil effect in both the first and second growth phase. We also show that the results obtained with inoculating sieved soil and with a soil suspension are not comparable. In conclusion, when designing plant–soil feedback experiments, it is crucial to consider that soil inoculum preparation can strongly influence the observed soil effect.
Plant species richness, identity and productivity differentially influence key groups of microbes in grassland soils of contrasting fertility.
Deyn, G.B. de; Quirk, H. ; Bardgett, R.D. - \ 2011
Biology Letters 7 (2011)1. - ISSN 1744-9561 - p. 75 - 78.
community composition - mycorrhizal fungi - diversity - biodiversity - carbon
The abundance of microbes in soil is thought to be strongly influenced by plant productivity rather than by plant species richness per se. However, whether this holds true for different microbial groups and under different soil conditions is unresolved. We tested how plant species richness, identity and biomass influence the abundances of arbuscular mycorrhizal fungi (AMF), saprophytic bacteria and fungi, and actinomycetes, in model plant communities in soil of low and high fertility using phospholipid fatty acid analysis. Abundances of saprophytic fungi and bacteria were driven by larger plant biomass in high diversity treatments. In contrast, increased AMF abundance with larger plant species richness was not explained by plant biomass, but responded to plant species identity and was stimulated by Anthoxantum odoratum. Our results indicate that the abundance of saprophytic soil microbes is influenced more by resource quantity, as driven by plant production, while AMF respond more strongly to resource composition, driven by variation in plant species richness and identity. This suggests that AMF abundance in soil is more sensitive to changes in plant species diversity per se and plant species composition than are abundances of saprophytic microbes
Association of Earthworm-Denitrifier Interactions with Increased Emission of Nitrous Oxide from Soil Mesocosms Amended with Crop Residue
Nebert, L.D. ; Bloem, J. ; Lubbers, I.M. ; Groenigen, J.W. van - \ 2011
Applied and Environmental Microbiology 77 (2011)12. - ISSN 0099-2240 - p. 4097 - 4104.
nosz genes - n2o-producing microorganisms - community composition - lumbricus-rubellus - microbial activity - agricultural soil - organic-matter - n2o emission - pcr data - carbon
Earthworm activity is known to increase emissions of nitrous oxide (N2O) from arable soils. Earthworm gut, casts, and burrows have exhibited higher denitrification activities than the bulk soil, implicating priming of denitrifying organisms as a possible mechanism for this effect. Furthermore, the earthworm feeding strategy may drive N2O emissions, as it determines access to fresh organic matter for denitrification. Here, we determined whether interactions between earthworm feeding strategy and the soil denitrifier community can predict N2O emissions from the soil. We set up a 90-day mesocosm experiment in which 15N-labeled maize (Zea mays L.) was either mixed in or applied on top of the soil in the presence or absence of the epigeic earthworm Lumbricus rubellus and/or the endogeic earthworm Aporrectodea caliginosa. We measured N2O fluxes and tested the bulk soil for denitrification enzyme activity and the abundance of 16S rRNA and denitrifier genes nirS and nosZ through real-time quantitative PCR. Compared to the control, L. rubellus increased denitrification enzyme activity and N2O emissions on days 21 and 90 (day 21, P = 0.034 and P = 0.002, respectively; day 90, P = 0.001 and P = 0.007, respectively), as well as cumulative N2O emissions (76%; P = 0.014). A. caliginosa activity led to a transient increase of N2O emissions on days 8 to 18 of the experiment. Abundance of nosZ was significantly increased (100%) on day 90 in the treatment mixture containing L. rubellus alone. We conclude that L. rubellus increased cumulative N2O emissions by affecting denitrifier community activity via incorporation of fresh residue into the soil and supplying a steady, labile carbon source
Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis
Salonen, A. ; Nikkilä, J. ; Jalanka-Tuovinen, J. ; Immonen, O. ; Rajilic-Stojanovic, M. ; Kekkonen, R.A. ; Palva, A. ; Vos, W.M. de - \ 2010
Journal of Microbiological Methods 81 (2010)2. - ISSN 0167-7012 - p. 127 - 134.
human gut microbiota - gradient gel-electrophoresis - 16s ribosomal-rna - real-time pcr - gastrointestinal-tract microbiota - human intestinal-tract - methanobrevibacter-smithii - community composition - metagenomic analysis - healthy-subjects
Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations >0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, including Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n=24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories.
Empirical and theoretical challenges in aboveground-belowground ecology
Putten, W.H. van der; Bardgett, R.D. ; Ruiter, P.C. de; Hol, W.H.G. ; Meyer, K.M. ; Bezemer, T.M. ; Bradford, M.A. ; Christensen, S. ; Eppinga, M.B. ; Fukami, T. ; Hemerik, L. ; Molofsky, J. ; Schädler, M. ; Scherber, C. ; Strauss, S.Y. ; Vos, M. ; Wardle, D.A. - \ 2009
Oecologia 161 (2009)1. - ISSN 0029-8549 - p. 1 - 14.
plant-soil feedback - increased competitive ability - climate-change - community composition - trophic interactions - insect herbivory - enemy release - food-web - terrestrial ecosystems - grassland ecosystems
A growing body of evidence shows that aboveground and belowground communities and processes are intrinsically linked, and that feedbacks between these subsystems have important implications for community structure and ecosystem functioning. Almost all studies on this topic have been carried out from an empirical perspective and in specific ecological settings or contexts. Belowground interactions operate at different spatial and temporal scales. Due to the relatively low mobility and high survival of organisms in the soil, plants have longer lasting legacy effects belowground than aboveground. Our current challenge is to understand how aboveground¿belowground biotic interactions operate across spatial and temporal scales, and how they depend on, as well as influence, the abiotic environment. Because empirical capacities are too limited to explore all possible combinations of interactions and environmental settings, we explore where and how they can be supported by theoretical approaches to develop testable predictions and to generalise empirical results. We review four key areas where a combined aboveground¿belowground approach offers perspectives for enhancing ecological understanding, namely succession, agro-ecosystems, biological invasions and global change impacts on ecosystems. In plant succession, differences in scales between aboveground and belowground biota, as well as between species interactions and ecosystem processes, have important implications for the rate and direction of community change. Aboveground as well as belowground interactions either enhance or reduce rates of plant species replacement. Moreover, the outcomes of the interactions depend on abiotic conditions and plant life history characteristics, which may vary with successional position. We exemplify where translation of the current conceptual succession models into more predictive models can help targeting empirical studies and generalising their results. Then, we discuss how understanding succession may help to enhance managing arable crops, grasslands and invasive plants, as well as provide insights into the effects of global change on community re-organisation and ecosystem processes
Fast response of lake plankton and nutrients to river inundations on floodplain lakes
Roozen, F.C.J.M. ; Peeters, E.T.H.M. ; Roijackers, R.M.M. ; Wyngaert, I.J.J. van den; Wolters, H. ; Coninck, H.C. de; Ibelings, B.W. ; Buijse, A.D. ; Scheffer, M. - \ 2008
River Research and Applications 24 (2008)4. - ISSN 1535-1459 - p. 388 - 406.
danube restoration project - lower rhine - hydrological connectivity - community composition - fresh-water - egg banks - phytoplankton - system - zooplankton - diversity
Key variables in ecosystems tend to operate on widely different time-scales. These time-scales become relevant when a disturbance rocks the ecosystem. Here we try to explain the fast dynamics of plankton and nutrients in the water column of floodplain lakes after disturbances (inundations). We take advantage of natural experiments, that is occasional massive overflow of floodplain lakes with river water. We sampled 10 lakes in two floodplains along the Dutch river Waal monthly for 3 years, capturing the impact of three inundation events. The inundations reset the plankton as well as chemical composition of most lakes to largely the same state. While biologically inert macro-ion data reflected a large and long lasting impact of the river water, dynamics of nutrients, phytoplankton and zooplankton communities between lakes diverged in a few weeks to regimes characteristic for the different lakes. While one spring inundation synchronized plankton dynamics to let the subsequent clear water phase occur at the same moment in different lakes, winter inundations did not have the same effect and apparently dynamics quickly diverged. Our results showed that effects of inundations and other processes that affect the state of the ecosystem should be studied considering the level of the slow components such as the sediment nutrient pool, fish stock and macrophyte communities. Plankton communities and lake water nutrient status give a practically instantaneous reflection of the condition of these slow components
Arthropod assemblages are best predicted by plant species composition
Schaffers, A.P. ; Raemakers, I.P. ; Sykora, K.V. ; Braak, C.J.F. ter - \ 2008
Ecology 89 (2008)3. - ISSN 0012-9658 - p. 782 - 794.
community composition - vegetation structure - grazing management - experimental tests - insect herbivores - diversity - habitat - biodiversity - grassland - classification
Insects and spiders comprise more than two-thirds of the Earth's total species diversity. There is wide concern, however, that the global diversity of arthropods may be declining even more rapidly than the diversity of vertebrates and plants. For adequate conservation planning, ecologists need to understand the driving factors for arthropod communities and devise methods that provide reliable predictions when resources do not permit exhaustive ground surveys. Which factor most successfully predicts arthropod community structure is still a matter of debate, however. The purpose of this study was to identify the factor best predicting arthropod assemblage composition. We investigated the species composition of seven functionally different arthropod groups (epigeic spiders, grasshoppers, ground beetles, weevils, hoppers, hoverflies, and bees) at 47 sites in The Netherlands comprising a range of seminatural grassland types and one heathland type. We then compared the actual arthropod composition with predictions based on plant species composition, vegetation structure, environmental data, flower richness, and landscape composition. For this we used the recently published method of predictive co-correspondence analysis, and a predictive variant of canonical correspondence analysis, depending on the type of predictor data. Our results demonstrate that local plant species composition is the most effective predictor of arthropod assemblage composition, for all investigated groups. In predicting arthropod assemblages, plant community composition consistently outperforms both vegetation structure and environmental conditions (even when the two are combined), and also performs better than the surrounding landscape. These results run against a common expectation of vegetation structure as the decisive factor. Such expectations, however, have always been biased by the fact that until recently no methods existed that could use an entire (plant) species composition in the explanatory role. Although more recent experimental diversity work has reawakened interest in the role of plant species, these studies still have not used (or have not been able to use) entire species compositions. They only consider diversity measures, both for plant and insect assemblages, which may obscure relationships. The present study demonstrates that the species compositions of insect and plant communities are clearly linked.
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