Stefan Ruyters

The Red Mud Accident in Ajka (Hungary): Plant Toxicity and Trace Metal Bioavailability in Red Mud Contaminated Soil

The red mud accident of October 4, 2010, in Ajka (Hungary) contaminated a vast area with caustic, saline red mud (pH 12) that contains several toxic trace metals above soil limits. Red mud was characterized and its toxicity for plants was measured to evaluate the soil contamination risks. Red mud radioactivity (e.g., (238)U) is about 10-fold above soil background and previous assessments revealed that radiation risk is limited to indoor radon. The plant toxicity and trace metal availability was tested with mixtures of this red mud and a local noncontaminated soil up to a 16% dry weight fraction. Increasing red mud applications increased soil pH to maximally 8.3 and soil solution EC to 12 dS m(-1). Shoot yield of barley seedlings was affected by 25% at 5% red mud in soil and above. Red mud increased shoot Cu, Cr, Fe, and Ni concentrations; however, none of these exceed toxic limits reported elsewhere. Moreover, NaOH amended reference treatments showed similar yield reductions and similar changes in shoot composition. Foliar diagnostics suggest that Na (>1% in affected plants) is the prime cause of growth effects in red mud and in corresponding NaOH amended soils. Shoot Cd and Pb concentrations decreased by increasing applications or were unaffected. Leaching amended soils (3 pore volumes) did not completely remove the Na injury, likely because soil structure was deteriorated. The foliar composition and the NaOH reference experiment allow concluding that the Na salinity, not the trace metal contamination, is the main concern for this red mud in soil.

Copper toxicity in soils under established vineyards in Europe: a survey.

Copper (Cu) containing fungicides have been used for more than one century in Europe on agricultural soils, such as vineyard soils. Total Cu concentrations in such soils can exceed toxicological limits that are commonly derived using artificially spiked soils. This study surveyed Cu toxicity in vineyard soils with reference to soils spiked with CuCl(2). Soil was collected in six established European vineyards. At each site, samples representing a Cu concentration gradient were collected. A control (uncontaminated) soil sampled nearby the vineyard was spiked with CuCl(2). Toxicity was tested using standard ecotoxicity tests: two plant assays (Lycopersicon esculentum Miller (tomato) and Hordeum vulgare L. (barley) growth), one microbial assay (nitrification) and one invertebrate assay (Enchytraeus albidus reproduction). Maximal total Cu concentrations in the vineyard sites ranged 435-690 mg Cu kg(-1), well above the local background (23-105 mg Cu kg(-1)). Toxicity in spiked soils (50% inhibition) was observed at added soil Cu concentrations from 190 to 1039 mg Cu kg(-1) (mean 540 mg Cu kg(-1)) depending on the assay and the site. In contrast, significant adverse effects were only found for three bioassays in vineyard samples of one site and for two bioassays in another site. Biological responses in these cases were more importantly explained by other soil properties than soil Cu. Overall, no Cu toxicity to plants, microbial processes and invertebrates was observed in vineyard soil samples at Cu concentrations well above European Union limits protecting the soil ecosystem.

Impact of primer choice on characterization of orchid mycorrhizal communities using 454 pyrosequencing.

Although the number of studies investigating mycorrhizal associations in orchids has increased in recent years, the fungal communities associating with orchids and how they differ between species and sites remain unclear. Recent research has indicated that individual orchid plants may associate with several fungi concurrently, implying that to study mycorrhizal associations in orchids the fungal community should be assessed, rather than the presence of individual dominant fungal species or strains. High‐throughput sequencing methods, such as 454 pyrosequencing, are increasingly used as the primary tool for such analyses. However, many studies combine universal primers from previous phylogenetic or ecological studies to generate amplicons suitable for 454 pyrosequencing without first critically evaluating their performance, potentially resulting in biased fungal community descriptions. Here, following in silico primer analysis we evaluated the performance of different combinations of existing PCR primers to characterize orchid mycorrhizal communities using 454 pyrosequencing by analysis of both an artificially assembled community of mycorrhizal fungi isolated from diverse orchid species and root samples from three different orchid species (Anacamptis morio, Ophrys tenthredinifera and Serapias lingua). Our results indicate that primer pairs ITS3/ITS4OF and ITS86F/ITS4, targeting the internal transcribed spacer‐2 (ITS‐2) region, outperformed other tested primer pairs in terms of number of reads, number of operational taxonomic units recovered from the artificial community and number of different orchid mycorrhizal associating families detected in the orchid samples. Additionally, we show the complementary specificity of both primer pairs, making them highly suitable for tandem use when studying the diversity of orchid mycorrhizal communities.

Phenotypic evaluation of natural and industrial Saccharomyces yeasts for different traits desirable in industrial bioethanol production

Saccharomyces cerevisiae is the organism of choice for many food and beverage fermentations because it thrives in high-sugar and high-ethanol conditions. However, the conditions encountered in bioethanol fermentation pose specific challenges, including extremely high sugar and ethanol concentrations, high temperature, and the presence of specific toxic compounds. It is generally considered that exploring the natural biodiversity of Saccharomyces strains may be an interesting route to find superior bioethanol strains and may also improve our understanding of the challenges faced by yeast cells during bioethanol fermentation. In this study, we phenotypically evaluated a large collection of diverse Saccharomyces strains on six selective traits relevant for bioethanol production with increasing stress intensity. Our results demonstrate a remarkably large phenotypic diversity among different Saccharomyces species and among S. cerevisiae strains from different origins. Currently applied bioethanol strains showed a high tolerance to many of these relevant traits, but several other natural and industrial S. cerevisiae strains outcompeted the bioethanol strains for specific traits. These multitolerant strains performed well in fermentation experiments mimicking industrial bioethanol production. Together, our results illustrate the potential of phenotyping the natural biodiversity of yeasts to find superior industrial strains that may be used in bioethanol production or can be used as a basis for further strain improvement through genetic engineering, experimental evolution, or breeding. Additionally, our study provides a basis for new insights into the relationships between tolerance to different stressors.

Bacterial community dynamics during industrial malting, with an emphasis on lactic acid bacteria.

Characterization of the microflora during malting is an essential step towards process management and optimization. Up till now, however, microbial characterization in the malting process has mostly been done using culture-dependent methods, probably leading to biased estimates of microbial diversity. The aim of this study was to characterize the bacterial communities using two culture-independent methods, including Terminal Restriction Fragment Length Polymorphism (T-RFLP) and 454 pyrosequencing, targeting the 16S rRNA gene. Studied samples originated from two harvest years and two malting houses malting the same batch of barley. Besides targeting the entire bacterial community (T-RFLP), emphasis was put on lactic acid bacteria (LAB) (T-RFLP and 454 pyrosequencing). The overall bacterial community richness was limited, but the community structure changed during the process. Zooming in on the LAB community using 454 pyrosequencing revealed a total of 47 species-level operational taxonomic units (OTUs). LAB diversity appeared relatively limited since 88% of the sequences were covered by the same five OTUs (representing members of Weissella, Lactobacillus and Leuconostoc) present in all samples investigated. Fluctuations in the relative abundances of the dominant LAB were observed with the process conditions. In addition, both the year of harvest and malting house influenced the LAB community structure.

Biosurfactant production by Pseudomonas strains isolated from floral nectar

To screen and identify biosurfactant‐producing Pseudomonas strains isolated from floral nectar; to characterize the produced biosurfactants; and to investigate the effect of different carbon sources on biosurfactant production.