Phylogenetische und funktionelle Diversität von Acidobacteria in Wald- und Grünlandböden unterschiedlicher Landnutzung

The identification of edaphic and biotic parameters influencing diversity and activity of Acidobacteria is a prerequisite to understand their role in soil biogeochemical cycles. Here, Acidobacteria diversity changes in grassland and forest soils of different landuse were assessed by sequencing and community fingerprints (T-RFLP) of 16S rRNA. Differences in Acidobacteria community composition were found between the study regions in Germany, between grassland and forest as well as between soil types and apart from soil moisture, carbon, nitrogen, ammonium and phosphorus content, Acidobacteria were predominantly influenced by soil pH. Furthermore, the diversity of Acidobacteria differed seasonally with highest diversity in October. Stable isotope probing was performed to follow the degradation of wheat residues in microcosms of a grassland and forest soil and to identify the bacteria involved by T-RFLP analysis and (pyro)sequencing of 16S rRNA. The wheat residue degrading microbial community was dominated by members of Actinobacteridae, α- and β-Proteobacteria, whereas Acidobacteria did not play a role in early degradation of plant residues

Phylogenetische und funktionelle Diversität von Acidobacteria in Wald- und Grünlandböden unterschiedlicher Landnutzung

The identification of edaphic and biotic parameters influencing diversity and activity of Acidobacteria is a prerequisite to understand their role in soil biogeochemical cycles. Here, Acidobacteria diversity changes in grassland and forest soils of different landuse were assessed by sequencing and community fingerprints (T-RFLP) of 16S rRNA. Differences in Acidobacteria community composition were found between the study regions in Germany, between grassland and forest as well as between soil types and apart from soil moisture, carbon, nitrogen, ammonium and phosphorus content, Acidobacteria were predominantly influenced by soil pH. Furthermore, the diversity of Acidobacteria differed seasonally with highest diversity in October. Stable isotope probing was performed to follow the degradation of wheat residues in microcosms of a grassland and forest soil and to identify the bacteria involved by T-RFLP analysis and (pyro)sequencing of 16S rRNA. The wheat residue degrading microbial community was dominated by members of Actinobacteridae, α- and β-Proteobacteria, whereas Acidobacteria did not play a role in early degradation of plant residues

Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions

peer-reviewedThe importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops

Phylogenetic and functional diversity of Acidobacteria in forest and grassland soils of different land use

The identification of edaphic and biotic parameters influencing diversity and activity of Acidobacteria is a prerequisite to understand their role in soil biogeochemical cycles. Here, Acidobacteria diversity changes in grassland and forest soils of different landuse were assessed by sequencing and community fingerprints (T-RFLP) of 16S rRNA. Differences in Acidobacteria community composition were found between the study regions in Germany, between grassland and forest as well as between soil types and apart from soil moisture, carbon, nitrogen, ammonium and phosphorus content, Acidobacteria were predominantly influenced by soil pH. Furthermore, the diversity of Acidobacteria differed seasonally with highest diversity in October. Stable isotope probing was performed to follow the degradation of wheat residues in microcosms of a grassland and forest soil and to identify the bacteria involved by T-RFLP analysis and (pyro)sequencing of 16S rRNA. The wheat residue degrading microbial community was dominated by members of Actinobacteridae, α- and β-Proteobacteria, whereas Acidobacteria did not play a role in early degradation of plant residues

Effect of Stacked Insecticidal Cry Proteins from Maize Pollen on Nurse Bees (Apis mellifera carnica) and Their Gut Bacteria

Honey bee pollination is a key ecosystem service to nature and agriculture. However, biosafety research on genetically modified crops rarely considers effects on nurse bees from intact colonies, even though they receive and primarily process the largest amount of pollen. The objective of this study was to analyze the response of nurse bees and their gut bacteria to pollen from Bt maize expressing three different insecticidal Cry proteins (Cry1A.105, Cry2Ab2, and Cry3Bb1). Naturally Cry proteins are produced by bacteria (Bacillus thuringiensis). Colonies of Apis mellifera carnica were kept during anthesis in flight cages on field plots with the Bt maize, two different conventionally bred maize varieties, and without cages, 1-km outside of the experimental maize field to allow ad libitum foraging to mixed pollen sources. During their 10-days life span, the consumption of Bt maize pollen had no effect on their survival rate, body weight and rates of pollen digestion compared to the conventional maize varieties. As indicated by ELISA-quantification of Cry1A.105 and Cry3Bb1, more than 98% of the recombinant proteins were degraded. Bacterial population sizes in the gut were not affected by the genetic modification. Bt-maize, conventional varieties and mixed pollen sources selected for significantly different bacterial communities which were, however, composed of the same dominant members, including Proteobacteria in the midgut and Lactobacillus sp. and Bifidobacterium sp. in the hindgut. Surprisingly, Cry proteins from natural sources, most likely B. thuringiensis, were detected in bees with no exposure to Bt maize. The natural occurrence of Cry proteins and the lack of detectable effects on nurse bees and their gut bacteria give no indication for harmful effects of this Bt maize on nurse honey bees

No Tangible Effects of Field-Grown Cisgenic Potatoes on Soil Microbial Communities

DNA modification techniques are increasingly applied to improve the agronomic performance of crops worldwide. Before cultivation and marketing, the environmental risks of such modified varieties must be assessed. This includes an understanding of their effects on soil microorganisms and associated ecosystem services. This study analyzed the impact of a cisgenic modification of the potato variety Desirée to enhance resistance against the late blight-causing fungus Phytophthora infestans (Oomycetes) on the abundance and diversity of rhizosphere inhabiting microbial communities. Two experimental field sites in Ireland and the Netherlands were selected, and for 2 subsequent years, the cisgenic version of Desirée was compared in the presence and absence of fungicides to its non-engineered late blight-sensitive counterpart and a conventionally bred late blight-resistant variety. At the flowering stage, total DNA was extracted from the potato rhizosphere and subjected to PCR for quantifying and sequencing bacterial 16S rRNA genes, fungal internal transcribed spacer (ITS) sequences, and nir genes encoding for bacterial nitrite reductases. Both bacterial and fungal communities responded to field conditions, potato varieties, year of cultivation, and bacteria sporadically also to fungicide treatments. At the Dutch site, without annual replication, fungicides stimulated nirK abundance for all potatoes, but with significance only for cisgenic Desirée. In all other cases, neither the abundance nor the diversity of any microbial marker differed between both Desirée versions. Overall, the study demonstrates environmental variation but also similar patterns of soil microbial diversity in potato rhizospheres and indicates that the cisgenic modification had no tangible impact on soil microbial communities.</p

Schematic figure on the incidence (A) and abundance (B) of bacterial phylotypes detected by T-RFLP based on 16S rRNA genes.

<p>The T-RF patterns for each treatment, i.e., exposure to Bt maize (BT), two conventional maize varieties (DKC, BEN) and mixed pollen sources including Phacelia (PHA), are based on 24 replicates from individual bees. Frequencies of incidences and abundances are indicated by squares and correlate with the grey scale. Abundance values in <b>B</b> indicate % of a particular T-RF in relation to total TRFs of the corresponding TRFP-profiles. Abundance values were averaged only from scored T-RFs. Significant differences in abundances of frequently occurring T-RFs are indicated with coloured boarder lines. Bacterial phylotypes indicated by the particular T-RFs were identified by DNA-sequencing (see also <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059589#pone.0059589.s004" target="_blank">Table S2</a>).</p

Hypothetical numbers of sporulated cells of <i>B. thuringiensis</i> strains expressing natural Cry proteins required for the detection of a Cry1A.105 equivalent by ELISA.

a<p>refers to an extraction volume of 300 µL; DTC, detection threshold was 0.5 mg mL^−1.</p

Nonmetric multidimensional scaling (NMDS) ordination plot of β-diversity patterns of bacterial community differences represented as Bray–Curtis distances of T-RFLP profiles.

<p>Stress values (0.21, 0.25) indicate that the distance between points in the ordination plot is a good representation of the degree of similarity between the bacterial communities in each sample. Each point represents the gut bacterial community obtained an individual nurse bee. Treatments: BT, exposure to pollen of Bt maize, DKC and BEN to conventional maize and PHA to other pollen sources including Phacelia.</p

Response of nurse bees after a 9 d exposure period either to Bt maize (treatment BT), or two conventional maize cultivars (DKC, BEN), or controls with <i>ad libitum</i> access to different pollen sources from colonies kept at a Phacelia field (PHA).

<p>The survival (A) was indicated by the retrieval rate of marked bees, their weight (B) was determined at the moment of their retrieval. Microscopic analysis of bee hindguts was performed to calculate a weighted average degree of maize pollen digestion (C). The error bars indicate 95% confidence intervals. *indicates significant difference of a specific treatment.</p