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Flemming Ekelund - One of the best experts on this subject based on the ideXlab platform.
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Local diversity of heathland Cercozoa explored by in-depth sequencing
The ISME journal, 2016Co-Authors: Christoffer Bugge Harder, Regin Rønn, David Bass, Asker Daniel Brejnrod, Waleed Abu Al-soud, Flemming EkelundAbstract:Cercozoa are abundant free-living Soil Protozoa and quantitatively important in Soil food webs; yet, targeted high-throughput sequencing (HTS) has not yet been applied to this group. Here we describe the development of a targeted assay to explore Cercozoa using HTS, and we apply this assay to measure Cercozoan community response to drought in a Danish climate manipulation experiment (two sites exposed to artificial drought, two unexposed). Based on a comparison of the hypervariable regions of the 18S ribosomal DNA of 193 named Cercozoa, we concluded that the V4 region is the most suitable for group-specific diversity analysis. We then designed a set of highly specific primers (encompassing ~270 bp) for 454 sequencing. The primers captured all major cercozoan groups; and >95% of the obtained sequences were from Cercozoa. From 443 350 high-quality short reads (>300 bp), we recovered 1585 operational taxonomic units defined by >95% V4 sequence similarity. Taxonomic annotation by phylogeny enabled us to assign >95% of our reads to order level and ~85% to genus level despite the presence of a large, hitherto unknown diversity. Over 40% of the annotated sequences were assigned to Glissomonad genera, whereas the most common individually named genus was the euglyphid Trinema. Cercozoan diversity was largely resilient to drought, although we observed a community composition shift towards fewer testate amoebae.
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Protozoan growth rates on secondary‐metabolite‐producing Pseudomonas spp. correlate with high‐level Protozoan taxonomy
FEMS microbiology letters, 2011Co-Authors: Annette L. Pedersen, Anne Winding, Andreas Altenburger, Flemming EkelundAbstract:Different features can protect bacteria against Protozoan grazing, for example large size, rapid movement, and production of secondary metabolites. Most papers dealing with these matters focus on bacteria. Here, we describe Protozoan features that affect their ability to grow on secondary-metabolite-producing bacteria, and examine whether different bacterial secondary metabolites affect Protozoa similarly. We investigated the growth of nine different Soil Protozoa on six different Pseudomonas strains, including the four secondary-metabolite-producing Pseudomonas fluorescens DR54 and CHA0, Pseudomonas chlororaphis MA342 and Pseudomonas sp. DSS73, as well as the two nonproducers P. fluorescens DSM50090T and P. chlororaphis ATCC43928. Secondary metabolite producers affected Protozoan growth differently. In particular, bacteria with extracellular secondary metabolites seemed more inhibiting than bacteria with membrane-bound metabolites. Interestingly, Protozoan response seemed to correlate with high-level Protozoan taxonomy, and amoeboid taxa tolerated a broader range of Pseudomonas strains than did the non-amoeboid taxa. This stresses the importance of studying both Protozoan and bacterial characteristics in order to understand bacterial defence mechanisms and potentially improve survival of bacteria introduced into the environment, for example for biocontrol purposes.
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Meeting on the Microbiology of Soils, Autumn 2001Estimation of Protozoan diversity in Soil
European Journal of Protistology, 2002Co-Authors: Flemming EkelundAbstract:Different methods of estimating Protozoan diversity in Soil are discussed in this paper, with the major emphasis on heterotrophic flagellates. Although many species of ciliates and testate amoebae seem to be unique to the Soil environment, the communities of heterotrophic flagellates and naked amoebae are probably best considered as restricted versions of their aquatic counterparts. Soil Protozoa are difficult to observe directly, hence culture techniques are usually used. These techniques enable us to explore certain functional aspects, but their major drawback is that some Soil Protozoa cannot be cultured. Molecular methods, however, have the potential to detect such non-culturable forms.
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Estimation of Protozoan diversity in Soil
European Journal of Protistology, 2002Co-Authors: Flemming EkelundAbstract:Different methods of estimating Protozoan diversity in Soil are discussed in this paper, with the major emphasis on heterotrophic flagellates. Although many species of ciliates and testate amoebae seem to be unique to theSoil environment, the communities of heterotrophic flagellates and naked amoebae are probably best considered as restricted versions of their aquatic counterparts. Soil Protozoa are difficult to observe directly, hence culture techniques are usually used. These techniques enable us to explore certain functional aspects, but their major drawback is that some Soil Protozoa cannot be cultured. Molecular methods, however, have the potential to detect such non-culturable forms.
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Population Dynamics of Active and Total Ciliate Populations in Arable Soil Amended with Wheat
Applied and environmental microbiology, 2002Co-Authors: Flemming Ekelund, Helle B. Frederiksen, Regin RønnAbstract:Soil Protozoa are characterized by their ability to produce cysts, which allows them to survive unfavorable conditions (e.g., desiccation) for extended periods. Under favorable conditions, they may rapidly excyst and begin feeding, but even under optimal conditions, a large proportion of the population may be encysted. The factors governing the dynamics of active and encysted cells in the Soil are not well understood. Our objective was to determine the dynamics of active and encysted populations of ciliates during the decomposition of freshly added organic material. We monitored, in Soil microcosms, the active and total populations of ciliates, their potential prey (bacteria and small Protozoa), their potential competitors (amoebae, flagellates, and nematodes), and their potential predators (nematodes). We sampled with short time intervals (2 to 6 days) and generated a data set, suitable for mathematical modeling. Following the addition of fresh organic material, bacterial numbers increased more than 1,400-fold. There was a temporary increase in the number of active ciliates, followed by a rapid decline, although the size of the bacterial prey populations remained high. During this initial burst of ciliate growth, the population of cystic ciliates increased 100-fold. We suggest that internal population regulation is the major factor governing ciliate encystment and that the rate of encystment depends on ciliate density. This model provides a quantitative explanation of ciliatostasis and can explain why Protozoan growth in Soil is less than that in aquatic systems. Internally governed encystment may be an essential adaptation to an unpredictable environment in which individual Protozoa cannot predict when the Soil will dry out and will survive desiccation only if they have encysted in time.
Anne Winding - One of the best experts on this subject based on the ideXlab platform.
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Effects of the Secondary Metabolite Producing Pseudomonas fluorescens CHA0 on Soil Protozoa and Bacteria
Acta Protozoologica, 2012Co-Authors: Anne Winding, Jana OberenderAbstract:Effects, BCA, secondary metabolite, Pseudomonas fluorescens CHA0, Soil, Protozoa, bacteria, PCR-DGGE
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Protozoan growth rates on secondary‐metabolite‐producing Pseudomonas spp. correlate with high‐level Protozoan taxonomy
FEMS microbiology letters, 2011Co-Authors: Annette L. Pedersen, Anne Winding, Andreas Altenburger, Flemming EkelundAbstract:Different features can protect bacteria against Protozoan grazing, for example large size, rapid movement, and production of secondary metabolites. Most papers dealing with these matters focus on bacteria. Here, we describe Protozoan features that affect their ability to grow on secondary-metabolite-producing bacteria, and examine whether different bacterial secondary metabolites affect Protozoa similarly. We investigated the growth of nine different Soil Protozoa on six different Pseudomonas strains, including the four secondary-metabolite-producing Pseudomonas fluorescens DR54 and CHA0, Pseudomonas chlororaphis MA342 and Pseudomonas sp. DSS73, as well as the two nonproducers P. fluorescens DSM50090T and P. chlororaphis ATCC43928. Secondary metabolite producers affected Protozoan growth differently. In particular, bacteria with extracellular secondary metabolites seemed more inhibiting than bacteria with membrane-bound metabolites. Interestingly, Protozoan response seemed to correlate with high-level Protozoan taxonomy, and amoeboid taxa tolerated a broader range of Pseudomonas strains than did the non-amoeboid taxa. This stresses the importance of studying both Protozoan and bacterial characteristics in order to understand bacterial defence mechanisms and potentially improve survival of bacteria introduced into the environment, for example for biocontrol purposes.
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Non-target effects of bacterial biological control agents on Soil Protozoa
Biology and Fertility of Soils, 2004Co-Authors: Karen Stevnbak Andersen, Anne WindingAbstract:Biological control agents (BCAs) have gained increasing interest as an alternative to chemical pesticides in agriculture. Before widespread environmental use, risk assessment of effects on target and non-target organisms are needed. However, the knowledge about the effect of BCAs on non-target Soil Protozoa is insufficient to support thorough risk assessment. In this study we report on the effects of Pseudomonas fluorescens DR54 that is a potential BCA active against root pathogenic fungi. We present evidence of negative effects of P. fluorescens DR54 on growth of the amoebae Hartmanella vermiformis and Acanthamoeba sp. cultures and natural assemblages of Soil Protozoans. The observed effects were larger than those of the P. fluorescens type strain DSM50090 and Enterobacter aerogenes SC and were tentatively attributed to viscosinamide, which is an antimicrobial compound with surfactant properties produced by P. fluorescens DR54.
Bland J. Finlay - One of the best experts on this subject based on the ideXlab platform.
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Soil Protozoa an intensive study of population dynamics and community structure in an upland grassland
Applied Soil Ecology, 2006Co-Authors: Genoveva F. Esteban, Ken J. Clarke, José L. Olmo, Bland J. FinlayAbstract:We focus on the key results from a 3-year intensive investigation of Soil Protozoan diversity sponsored by the Natural Environment Research Council (UK). The investigation enabled us to study simultaneously all major Protozoan groups at a single site—the 1 ha area of upland grassland at the Macaulay Land Use Research Institute’s Sourhope Research Station in Southern Scotland. A total of 365 Protozoan species were recorded, in four broad taxonomic groups—ciliates, testate amoebae, naked amoebae and flagellates. We explored the natural history of these groups, recording species richness, growth rates, and absolute abundance, as well as community structures within the context of the fractal character of the Soil. We developed methods for estimating the abundance and growth potential of the Soil Protozoan community, plus seasonal variation in Protozoan abundance within taxonomic groups. We isolated new species, re-described others, and produced a guide to the identification of testate amoebae in Soil. We produced evidence for the ubiquitous random dispersal of Soil Protozoa, and we found no evidence for geographically restricted distributions at spatial scales ranging from 4 m 2 to global. Roughly one quarter of global free-living Protozoan diversity was recorded from this 1 ha site. Local and global abundances were correlated—i.e. species that are locally rare tend to be globally rare, and those that are locally abundant tend to be globally abundant. # 2006 Elsevier B.V. All rights reserved.
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Soil Protozoa—An intensive study of population dynamics and community structure in an upland grassland §
Applied Soil Ecology, 2006Co-Authors: Genoveva F. Esteban, Ken J. Clarke, José L. Olmo, Bland J. FinlayAbstract:We focus on the key results from a 3-year intensive investigation of Soil Protozoan diversity sponsored by the Natural Environment Research Council (UK). The investigation enabled us to study simultaneously all major Protozoan groups at a single site—the 1 ha area of upland grassland at the Macaulay Land Use Research Institute’s Sourhope Research Station in Southern Scotland. A total of 365 Protozoan species were recorded, in four broad taxonomic groups—ciliates, testate amoebae, naked amoebae and flagellates. We explored the natural history of these groups, recording species richness, growth rates, and absolute abundance, as well as community structures within the context of the fractal character of the Soil. We developed methods for estimating the abundance and growth potential of the Soil Protozoan community, plus seasonal variation in Protozoan abundance within taxonomic groups. We isolated new species, re-described others, and produced a guide to the identification of testate amoebae in Soil. We produced evidence for the ubiquitous random dispersal of Soil Protozoa, and we found no evidence for geographically restricted distributions at spatial scales ranging from 4 m 2 to global. Roughly one quarter of global free-living Protozoan diversity was recorded from this 1 ha site. Local and global abundances were correlated—i.e. species that are locally rare tend to be globally rare, and those that are locally abundant tend to be globally abundant. # 2006 Elsevier B.V. All rights reserved.
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Biodiversity of terrestrial Protozoa appears homogeneous across local and global spatial scales.
Protist, 2001Co-Authors: Bland J. Finlay, Genoveva F. Esteban, Ken J. Clarke, José L. OlmoAbstract:Summary Free-living microbes are by far the most abundant group of organisms in the biosphere, yet estimates of global species richness remain nebulous, and there is no consensus regarding the likely geographical distribution of species. Both uncertainties are addressed by the suggestion that the vast abundance of microbes may drive their ubiquitous random dispersal; for this would also make it likely that global species richness is relatively low. Here we test the idea of ubiquitous dispersal of testate amoebae and ciliates living in Soil. We analysed their abundance and species richness in 150 Soil samples collected from the one-hectare grassland site at Sourhope in Scotland, and in comparable published data from 1500 Soil samples collected worldwide. Following taxonomic revision and removal of synonyms, there remained a total of 186 taxa (91 testate and 95 ciliate) recorded from both Sourhope and other places in the world. A fundamental pattern of random spatial distribution of species was revealed in species that are relatively rare. This probably arises from random dispersal, for when localised population growth occurs, the distributions become aggregated, as in virtually all metazoan species. We find no evidence for geographically-restricted Protozoan morphospecies at spatial scales of 4 m 2 , 10,000 m 2 , or worldwide. Species that are locally rare or abundant are similarly rare or abundant on a global scale. Approximately one third of the global diversity of Soil Protozoa was found at the one-hectare grassland site in Scotland, but this is a minimum figure, for recorded species richness is proportional to sampling effort, as shown here.
Bryan S. Griffiths - One of the best experts on this subject based on the ideXlab platform.
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Spatial distribution of Soil Protozoa in an upland grassland
European Journal of Protistology, 2002Co-Authors: Bryan S. GriffithsAbstract:A 12 x 12 m plot from a visually uniform upland pasture was sampled in a spatially referenced manner. There was no correlation between inter-sample distance and the Protozoan community (colpodid and heterotrich ciliates, flagellates, naked amoebae, and total biomass). Evidence from the other parameters measured, and from other studies reported in the literature, indicates that spatial organisation in Protozoan communities occurs at scales below 10cm.
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Meeting on the Microbiology of Soils, Autumn 2001Spatial distribution of Soil Protozoa in an upland grassland
European Journal of Protistology, 2002Co-Authors: Bryan S. GriffithsAbstract:A 12 × 12 m plot from a visually uniform upland pasture was sampled in a spatially referenced manner. There was no correlation between inter-sample distance and the Protozoan community (colpodid and heterotrich ciliates, flagellates, naked amoebae, and total biomass). Evidence from the other parameters measured, and from other studies reported in the literature, indicates that spatial organisation in Protozoan communities occurs at scales below 10 cm.
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Impact of Protozoan Grazing on Bacterial Community Structure in Soil Microcosms
Applied and environmental microbiology, 2002Co-Authors: Regin Rønn, Bryan S. Griffiths, A. E. Mccaig, James I. ProsserAbstract:The influence of grazing by a mixed assemblage of Soil Protozoa (seven flagellates and one amoeba) on bacterial community structure was studied in Soil microcosms amended with a particulate resource (sterile wheat roots) or a soluble resource (a solution of various organic compounds). Sterilized Soil was reinoculated with mixed Soil bacteria (obtained by filtering and dilution) or with bacteria and Protozoa. Denaturing gradient gel electrophoresis (DGGE) of PCR amplifications of 16S rRNA gene fragments, as well as community level physiological profiling (Biolog plates), suggested that the mixed Protozoan community had significant effects on the bacterial community structure. Excising and sequencing of bands from the DGGE gels indicated that high-G+C gram-positive bacteria closely related to Arthrobacter spp. were favored by grazing, whereas the excised bands that decreased in intensity were related to gram-negative bacteria. The percentages of intensity found in bands related to high G+C gram positives increased from 4.5 and 12.6% in the ungrazed microcosms amended with roots and nutrient solution, respectively, to 19.3 and 32.9% in the grazed microcosms. Protozoa reduced the average bacterial cell size in microcosms amended with nutrient solution but not in the treatment amended with roots. Hence, size-selective feeding may explain some but not all of the changes in bacterial community structure. Five different Protozoan isolates (Acanthamoeba sp., two species of Cercomonas, Thaumatomonas sp., and Spumella sp.) had different effects on the bacterial communities. This suggests that the composition of Protozoan communities is important for the effect of Protozoan grazing on bacterial communities.
Annette L. Pedersen - One of the best experts on this subject based on the ideXlab platform.
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Protozoan growth rates on secondary‐metabolite‐producing Pseudomonas spp. correlate with high‐level Protozoan taxonomy
FEMS microbiology letters, 2011Co-Authors: Annette L. Pedersen, Anne Winding, Andreas Altenburger, Flemming EkelundAbstract:Different features can protect bacteria against Protozoan grazing, for example large size, rapid movement, and production of secondary metabolites. Most papers dealing with these matters focus on bacteria. Here, we describe Protozoan features that affect their ability to grow on secondary-metabolite-producing bacteria, and examine whether different bacterial secondary metabolites affect Protozoa similarly. We investigated the growth of nine different Soil Protozoa on six different Pseudomonas strains, including the four secondary-metabolite-producing Pseudomonas fluorescens DR54 and CHA0, Pseudomonas chlororaphis MA342 and Pseudomonas sp. DSS73, as well as the two nonproducers P. fluorescens DSM50090T and P. chlororaphis ATCC43928. Secondary metabolite producers affected Protozoan growth differently. In particular, bacteria with extracellular secondary metabolites seemed more inhibiting than bacteria with membrane-bound metabolites. Interestingly, Protozoan response seemed to correlate with high-level Protozoan taxonomy, and amoeboid taxa tolerated a broader range of Pseudomonas strains than did the non-amoeboid taxa. This stresses the importance of studying both Protozoan and bacterial characteristics in order to understand bacterial defence mechanisms and potentially improve survival of bacteria introduced into the environment, for example for biocontrol purposes.