A strictly anaerobic betaproteobacterium Georgfuchsia toluolica gen. nov., sp. nov. degrades aromatic compounds with Fe(III), Mn(IV) or nitrate as an electron acceptor

A bacterium (strain G5G6) that grows anaerobically with toluene was isolated from a polluted aquifer (Banisveld, the Netherlands). The bacterium uses Fe(III), Mn(IV) and nitrate as terminal electron acceptors for growth on aromatic compounds. The bacterium does not grow on sugars, lactate or acetate. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain G5G6 belonged to the Betaproteobacteria . Its closest, but only distantly related, cultured relative is Sterolibacterium denitrificans Chol-1S^T (94.6% similarity of the 16S rRNA genes), a cholesterol-oxidizing, denitrifying bacterium. Strain G5G6 possesses the benzylsuccinate synthase A ( bssA ) gene encoding the α-subunit of Bss, which catalyzes the first step in anaerobic toluene degradation. The deduced BssA amino acid sequence is closely related to those of Azoarcus and Thauera species, which also belong to the Betaproteobacteria . Strain G5G6 is the first toluene-degrading, iron-reducing bacterium that does not belong to the Geobacteraceae within the Deltaproteobacteria . Based on phylogenetic and physiological comparison, strain G5G6 could not be assigned to a described species. Therefore, strain G5G6 (DSMZ 19032^T=JCM 14632^T) is a novel taxon of the Betaproteobacteria . We propose the name Georgfuchsia toluolica gen. nov., sp. nov.     

Interdisciplinary integration in biology? An overview

Philosophical theories about reduction and integration in science are at variance with what is happenign in science. A realistic approach to science show that possibilities for reduction and integration are limited. The classical ideal of a unified science has since long been rejected in philosophy. But the current emphasis on interdisciplinary integration in philosophy and in science shows that it survives in a different guise. It is necessary to redress the balance, specifically in biology. Methodological analysis shows that many of the grand interdisciplinary theories involving biology actually represent pseudo-integration covered up by inappropriate, overgeneral concepts. Integrationism is not bad, but it must be kept within reasonable bounds. If the present analysis is appropriate, there will have to be fundamental changes in research strategy both in science and in the philosophy of science.     

Contrasting dynamics of ciliate communities in sandy and silty sediments of an estuarine intertidal flat

During a 1-year study of the ciliate faunas of a silty and a sandy site on an intertidal flat in the Westerschelde estuary, a total number of 107 taxa were recorded belonging to at least 52 genera and 15 orders. Our results suggest that physical properties of the sediment were more important in regulating ciliate abundance, diversity and community composition than food availability, predation, temperature or oxygen concentration. Ciliate abundance and diversity were positively related to sediment grain size and the ciliate community of silty sediments was found to be a subset of that of sandy sediments. At the sandy site, where the sediment composition was stable, seasonal changes in the ciliate community were related to changes in food availability and/or temperature. At both the sandy and silty sites, a clear vertical gradient in the ciliate community was observed that appeared to be linked to gradients in food availability and oxygen concentration. These vertical gradients in ciliate community composition, however, were less steep than the measured oxygen gradients, probably due to the presence of oxic microniches in the anoxic zone.     

Alterations in cell membrane properties caused by perfluorinated compounds

The recent detection of perfluorinated compounds (PFCs) in wildlife from even remote locations has spurred interest in the environmental occurrence and effects of these chemicals. While the global distribution of PFCs is increasingly understood, there is still little information available on their effects on wildlife. The amphiphillic nature of PFCs suggests that their effects could be primarily on cell membranes. In this study we measured the effects of PFCs on membrane fluidity and mitochondrial membrane potential using flow cytometry and effects on membrane permeability using cell bioassay procedures (H4IIE, MCF-7, PLHC-1). Of the PFCs tested, only perfluorooctane sulfonic acid (PFOS) increased the permeability of cell membranes to the hydrophobic ligands used. Three PFCs were tested in the membrane fluidity assay: PFOS, perfluorohexane sulfonic acid (PFHS), and perfluorobutane sulfonic acid (PFBS). PFOS increased membrane fluidity in fish leukocytes in a dose-dependent fashion, while PFHS and PFBS had no effect in the concentration range tested. The lowest effective concentrations for the membrane fluidity effects of PFOS were 5-15 mg/l. Effects on mitochondrial membrane potential occurred in the same concentration range as effects on membrane fluidity. This suggests that PFOS effects membrane properties at concentrations below those associated with other adverse effects.     

Interactions between spatially separated herbivores indirectly alter plant diversity

Above‐ and belowground herbivores promote plant diversity when selectively feeding on dominant plant species, but little is known about their combined effects. Using a model system, we show that neutral effects of an aboveground herbivore and positive effects of a belowground herbivore on plant diversity became profoundly negative when adding these herbivores in combination. The non‐additive effects were explained by differences in plant preference between the aboveground‐ and the belowground herbivores and their consequences for indirect interactions among plant species. Simultaneous exposure to aboveground‐ and belowground herbivores led to plant communities being dominated by a few highly abundant species. As above‐ and belowground invertebrate herbivores generally differ in their mobility and local distribution patterns, our results strongly suggest that aboveground–belowground interactions contribute to local spatial heterogeneity of diversity patterns within plant communities.     

First isolation of hepatitis E virus genotype 4 in Europe through swine surveillance in the Netherlands and Belgium

Hepatitis E virus (HEV) genotypes 3 and 4 are a cause of human hepatitis and swine are considered the main reservoir. To study the HEV prevalence and characterize circulating HEV strains, fecal samples from swine in the Netherlands and Belgium were tested by RT-PCR. HEV prevalence in swine was 7-15%. The Dutch strains were characterized as genotype 3, subgroups 3a, 3c and 3f, closely related to sequences found in humans and swine earlier. The HEV strains found in Belgium belonged to genotypes 3f and 4b. The HEV genotype 4 strain was the first ever reported in swine in Europe and an experimental infection in pigs was performed to isolate the virus. The genotype 4 strain readily infected piglets and caused fever and virus shedding. Since HEV4 infections have been reported to run a more severe clinical course in humans this observation may have public health implications.     

Signal peptide hydrophobicity is critical for early stages in protein export by Bacillus subtilis

Signal peptides that direct protein export in Bacillus subtilis are overall more hydrophobic than signal peptides in Escherichia coli. To study the importance of signal peptide hydrophobicity for protein export in both organisms, the alpha-amylase AmyQ was provided with leucine-rich (high hydrophobicity) or alanine-rich (low hydrophobicity) signal peptides. AmyQ export was most efficiently directed by the authentic signal peptide, both in E. coli and B. subtilis. The leucine-rich signal peptide directed AmyQ export less efficiently in both organisms, as judged from pulse-chase labelling experiments. Remarkably, the alanine-rich signal peptide was functional in protein translocation only in E. coli. Cross-linking of in vitro synthesized ribosome nascent chain complexes (RNCs) to cytoplasmic proteins showed that signal peptide hydrophobicity is a critical determinant for signal peptide binding to the Ffh component of the signal recognition particle (SRP) or to trigger factor, not only in E. coli, but also in B. subtilis. The results show that B. subtilis SRP can discriminate between signal peptides with relatively high hydrophobicities. Interestingly, the B. subtilis protein export machinery seems to be poorly adapted to handle alanine-rich signal peptides with a low hydrophobicity. Thus, signal peptide hydrophobicity appears to be more critical for the efficiency of early stages in protein export in B. subtilis than in E. coli.     

Soil fauna diversity increases CO2 but suppresses N2O emissions from soil

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.