ORCID Profile
0000-0003-3866-0832
Current Organisation
Universiteit Utrecht
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Publisher: Wiley
Date: 28-01-2021
DOI: 10.1111/GCB.15471
Abstract: Ecosystems integrity and services are threatened by anthropogenic global changes. Mitigating and adapting to these changes require knowledge of ecosystem functioning in the expected novel environments, informed in large part through experimentation and modelling. This paper describes 13 advanced controlled environment facilities for experimental ecosystem studies, herein termed ecotrons, open to the international community. Ecotrons enable simulation of a wide range of natural environmental conditions in replicated and independent experimental units while measuring various ecosystem processes. This capacity to realistically control ecosystem environments is used to emulate a variety of climatic scenarios and soil conditions, in natural sunlight or through broad‐spectrum lighting. The use of large ecosystem s les, intact or reconstructed, minimizes border effects and increases biological and physical complexity. Measurements of concentrations of greenhouse trace gases as well as their net exchange between the ecosystem and the atmosphere are performed in most ecotrons, often quasi continuously. The flow of matter is often tracked with the use of stable isotope tracers of carbon and other elements. Equipment is available for measurements of soil water status as well as root and canopy growth. The experiments ran so far emphasize the ersity of the hosted research. Half of them concern global changes, often with a manipulation of more than one driver. About a quarter deal with the impact of bio ersity loss on ecosystem functioning and one quarter with ecosystem or plant physiology. We discuss how the methodology for environmental simulation and process measurements, especially in soil, can be improved and stress the need to establish stronger links with modelling in future projects. These developments will enable further improvements in mechanistic understanding and predictive capacity of ecotron research which will play, in complementarity with field experimentation and monitoring, a crucial role in exploring the ecosystem consequences of environmental changes.
Publisher: American Chemical Society (ACS)
Date: 27-06-2018
Abstract: Material flow analysis shows that soil is a key repository for silver (Ag) from (nano)silver-functionalized consumer products, but the potential effects of Ag toxicity, via Ag
Publisher: Frontiers Media SA
Date: 10-02-2016
Publisher: Springer Science and Business Media LLC
Date: 06-2012
DOI: 10.1038/NBT.2235
Publisher: Springer Science and Business Media LLC
Date: 12-03-2008
Publisher: Wiley
Date: 07-11-2013
DOI: 10.1111/GCB.12045
Abstract: Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO2 emissions. Short-term atmospheric elevated CO2 exposure has been shown to create major shifts in C flow routes and ersity of the active soil-borne microbial community. Long-term increases in CO2 have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO2 exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO2 concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by (13) C pulse-chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA-stable isotope probing (RNA-SIP), in combination with real-time PCR and PCR-DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO2 was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO2 caused a continuous increase in the (13) C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO2 conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.
Publisher: Springer Science and Business Media LLC
Date: 05-2008
DOI: 10.1038/NBT1360
Publisher: Springer Science and Business Media LLC
Date: 16-07-2008
Publisher: Wiley
Date: 21-08-2007
Publisher: Springer Science and Business Media LLC
Date: 18-06-2009
Abstract: Soil community responses to increased atmospheric CO(2) concentrations are expected to occur mostly through interactions with changing vegetation patterns and plant physiology. To gain insight into the effects of elevated atmospheric CO(2) on the composition and functioning of microbial communities in the rhizosphere, Carex arenaria (a non-mycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown under defined atmospheric conditions with either ambient (350 p.p.m.) or elevated (700 p.p.m.) CO(2) concentrations. PCR-DGGE (PCR-denaturing gradient gel electrophoresis) and quantitative-PCR were carried out to analyze, respectively, the structure and abundance of the communities of actinomycetes, Fusarium spp., Trichoderma spp., Pseudomonas spp., Burkholderia spp. and Bacillus spp. Responses of specific functional groups, such as phloroglucinol, phenazine and pyrrolnitrin producers, were also examined by quantitative-PCR, and HPLC (high performance liquid chromatography) was employed to assess changes in exuded sugars in the rhizosphere. Multivariate analysis of group-specific community profiles showed disparate responses to elevated CO(2) for the different bacterial and fungal groups examined, and these responses were dependent on plant type and soil nutrient availability. Within the bacterial community, the genera Burkholderia and Pseudomonas, typically known as successful rhizosphere colonizers, were significantly influenced by elevated CO(2), whereas the genus Bacillus and actinomycetes, typically more dominant in bulk soil, were not. Total sugar concentrations in the rhizosphere also increased in both plants in response to elevated CO(2). The abundances of phloroglucinol-, phenazine- and pyrrolnitrin-producing bacterial communities were also influenced by elevated CO(2), as was the abundance of the fungal genera Fusarium and Trichoderma.
Publisher: Wiley
Date: 18-03-2013
Publisher: Elsevier
Date: 2007
Publisher: Proceedings of the National Academy of Sciences
Date: 06-2010
Abstract: Rising atmospheric CO 2 levels are predicted to have major consequences on carbon cycling and the functioning of terrestrial ecosystems. Increased photosynthetic activity is expected, especially for C-3 plants, thereby influencing vegetation dynamics however, little is known about the path of fixed carbon into soil-borne communities and resulting feedbacks on ecosystem function. Here, we examine how arbuscular mycorrhizal fungi (AMF) act as a major conduit in the transfer of carbon between plants and soil and how elevated atmospheric CO 2 modulates the belowground translocation pathway of plant-fixed carbon. Shifts in active AMF species under elevated atmospheric CO 2 conditions are coupled to changes within active rhizosphere bacterial and fungal communities. Thus, as opposed to simply increasing the activity of soil-borne microbes through enhanced rhizodeposition, elevated atmospheric CO 2 clearly evokes the emergence of distinct opportunistic plant-associated microbial communities. Analyses involving RNA-based stable isotope probing, neutral hosphate lipid fatty acids stable isotope probing, community fingerprinting, and real-time PCR allowed us to trace plant-fixed carbon to the affected soil-borne microorganisms. Based on our data, we present a conceptual model in which plant-assimilated carbon is rapidly transferred to AMF, followed by a slower release from AMF to the bacterial and fungal populations well-adapted to the prevailing (myco-)rhizosphere conditions. This model provides a general framework for reappraising carbon-flow paths in soils, facilitating predictions of future interactions between rising atmospheric CO 2 concentrations and terrestrial ecosystems.
Publisher: Springer Science and Business Media LLC
Date: 23-04-2009
Abstract: Biological ammonia oxidation had long been thought to be mediated solely by discrete clades of beta- and gamma-proteobacteria (ammonia-oxidizing bacteria AOB). However, ammonia-oxidizing Crenarchaeota (ammonia-oxidizing archaea AOA) have recently been identified and proposed to be the dominant agents of ammonia oxidation in soils. Nevertheless, the dynamics of AOB versus AOA, and their relative contribution to soil ammonia oxidation and ecosystem functioning on stress and environmental perturbation, remain unknown. Using a 3-year longitudinal field study and the amoA gene as a molecular marker, we demonstrate that AOB, but not AOA, mediate recovery of nitrification after zinc (Zn) contamination. Pristine soils showed approximately equal amoA gene copy numbers and transcript levels for AOB and AOA. At an intermediate Zn dose (33.7 mmol Zn per kg), ammonia oxidation was completely inhibited, and the numbers of AOB and AOA amoA gene copies and gene transcripts were reduced. After 2 years, ammonia oxidation in the field soils was fully restored to preexposure levels, and this restoration of function was concomitant with an increase of AOB amoA gene copy and gene transcript numbers. Analysis of the restored community revealed domination by a phylogenetically distinct Zn-tolerant Nitrosospira sp. community. In contrast, the numbers of AOA amoA gene copies and gene transcripts remained 3- and 10(4)-fold lower than recovered AOB values, respectively. Thus, although recent findings have emphasized a dominant role of archaea in soil-borne ammonia oxidation, we demonstrate that a phylogenetic shift within the AOB community drives recovery of nitrification from Zn contamination in this soil.
Publisher: Wiley
Date: 12-08-2008
DOI: 10.1111/J.1462-2920.2008.01644.X
Abstract: Climatic changes will not only result in higher overall temperature, but also in greater variability in weather conditions. Antarctic soils are subjected to extremely variable conditions in the form of frequent freeze-thaw cycles (FTCs), but the importance of alteration in FTC frequency, compared with increases in average temperature and indirect vegetation-mediated effects on soil microorganisms, is still unknown. We therefore designed two complementary microcosm experiments using undisturbed soil cores from Signy Island (60 degrees 43'S, 45 degrees 38'W) in the maritime Antarctic. The experiments consisted of soil core incubations with or without the overlying vegetation at four different temperatures and six different FTC regimes. We assessed bacterial and fungal density and community structure, as well as the density of several key genes in microbial nutrient cycles using a combination of RNA- and DNA-based molecular fingerprinting and quantitative PCR approaches in addition to enzymatic activity assays. Results showed that bacteria were more affected by warming than by changes in FTC frequency. In contrast, fungal community structure and abundance were mostly influenced by FTC frequency, as well as the presence of vegetation cover. The relative densities of several bacterial gene families involved in key steps of the N-cycle were affected by FTCs, while warming had little or no effect. The FTCs and incubation temperature also strongly influenced laccase enzymatic activity in soil. In total, our results suggest that, in addition to climatic warming, increased climatic variability may also have a profound impact on Antarctic microbial communities. Although these effects are difficult to detect with assays of total bacterial community structure, they do become manifest in the analysis of key functional gene densities.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 12-08-2011
Abstract: Plants and their associated fungi reward partners that offer the best resources to sustain mutualism in complex systems.
Publisher: Wiley
Date: 10-06-2019
Abstract: Predicting changes in plant ersity in response to human activities represents one of the major challenges facing ecologists and land managers striving for sustainable ecosystem management. Classical field studies have emphasized the importance of community primary productivity in regulating changes in plant species richness. However, experimental studies have yielded inconsistent empirical evidence, suggesting that primary productivity is not the sole determinant of plant ersity. Recent work has shown that more accurate predictions of changes in species ersity can be achieved by combining measures of species’ cover and height into an index of space resource utilization (SRU). While the SRU approach provides reliable predictions, it is time‐consuming and requires extensive taxonomic expertise. Ecosystem processes and plant community structure are likely driven primarily by dominant species (mass ratio effect). Within communities, it is likely that dominant and rare species have opposite contributions to overall bio ersity trends. We, therefore, suggest that better species richness predictions can be achieved by utilizing SRU assessments of only the dominant species (SRU D ), as compared to SRU or biomass of the entire community. Here, we assess the ability of these measures to predict changes in plant ersity as driven by nutrient addition and herbivore exclusion. First, we tested our hypotheses by carrying out a detailed analysis in an alpine grassland that measured all species within the community. Next, we assessed the broader applicability of our approach by measuring the first three dominant species for five additional experimental grassland sites across a wide geographic and habitat range. We show that SRU D outperforms community biomass, as well as community SRU, in predicting bio ersity dynamics in response to nutrients and herbivores in an alpine grassland. Across our additional sites, SRU D yielded far better predictions of changes in species richness than community biomass, demonstrating the robustness and generalizable nature of this approach. Synthesis. The SRU D approach provides a simple, non‐destructive and more accurate means to monitor and predict the impact of global change drivers and management interventions on plant communities, thereby facilitating efforts to maintain and recover plant ersity.
No related grants have been discovered for George Kowalchuk.