Identification of novel Crenarchaeota and Euryarchaeota clusters associated with different depth layers of a forest soil

Archaea have been shown to be ubiquitous among soil microbial communities. However, our knowledge on their diversity and spatial distribution in soil ecosystems is still limited. This study was conducted to investigate archaeal community changes along a forest soil depth profile in Unterehrendingen, Switzerland. From four consecutive soil depth layers, bulk soil DNA was extracted. Archaea-specific PCR amplification of small subunit ribosomal RNA genes (rDNA) was performed and combined with restriction fragment length polymorphism (RFLP) analysis with restriction endonuclease HaeIII [Bundt et al., Soil Biol. Biochem. 33 (2001) 729-738]. Significant changes of the RFLP fingerprints were reproducibly observed from the soil surface to 1 m depth. From the surface soil layer (0-9 cm) and the bottom soil layer (50-100 cm), libraries of PCR-amplified archaeal rDNA fragments were constructed. Screening of the libraries yielded various clones of different HaeIII RFLP types from the surface and the bottom soil layers, revealing shifts in major archaeal components along the soil depth profile. Clones of all RFLP types were sequenced and phylogenetically affiliated. These analyses revealed even more pronounced Archaea community shifts along the depth gradient. Several novel soil archaeal clusters were identified and some appeared predominantly associated to either the surface or the bottom soil layer. Euryarchaeal rDNA sequences, not yet reported from aerated soils, were found in the surface soil layer and were affiliated to the order Thermoplasmales and relatives. Novel crenarchaeal soil clusters were identified that included sequences only retrieved from the bottom soil layer. In this study, a this far unreported variety of archaeal groups was found in a forest soil ecosystem. The distinct depth-related community shift suggested the occurrence of different archaeal types that depend on environmental parameters that change along the soil depth profil

Molecular diversity of the Metarhizium anisopliae lineage in an agricultural field

Entomopathogenic fungal isolates identified by morphology as Metarhizium anisopliae may belong to different species when identified by molecular characters. We isolated Metarhizium spp. from an experimental agricultural field under both conventional and organic farming regimes using Tenebrio molitor as bait insect to assess the molecular diversity within the soil. Isolates were analyzed using DNA sequencing and applying SSR markers. Within the former M. anisopliae lineage, we found M. brunneum (86.3%), M. robertsii (11.3%) and M. majus (3.4%) in the soil samples. Several genotypes of each species were identified based on SSR markers. Differences in abundance of the species and their genotypes suggest different adaptations to the soil environment of the agricultural field. There were no effects of conventinal or organic farming regimes on diversity of the fungi

Swiss Mattenklee landraces, a distinct and diverse genetic resource of red clover (Trifolium pratense L.)

Genetic variability within and among 19 landraces and cultivars of red clover (Trifolium pratense L.) was investigated by means of amplified fragment length polymorphism (AFLP) analysis in order to assess the potential value of Swiss Mattenklee landraces as genetic resources for plant breeding and the preservation of biodiversity. Populations were classified into three groups according to their origin and agronomic features: Mattenklee landraces (8), Mattenklee cultivars (8) and field clover cultivars (3). Analysis of molecular variance based on 276 polymorphic AFLP markers revealed 80% of total variability to be due to variability within populations while 12% were attributed to variability among groups. Stepwise discriminant analysis identified a subset of 126 AFLP markers which best separated individual plants into the three respective groups. Genetic distances between populations were considerably larger among groups than among populations within the same group, providing further evidence for the genetic distinction between Mattenklee landraces, Mattenklee cultivars and field clover cultivars. AFLP markers identified two landrace clusters, containing three and four populations respectively, which, together with one additional landrace, may sufficiently represent the genetic variability of all eight landraces investigated. The results of this study strongly suggest that Swiss Mattenklee landraces form a genetically distinct group of red clover. The data obtained provide criteria on how to efficiently manage, preserve and exploit Mattenklee germplasm

Identification of dominant bacterial phylotypes in a cadmium-treated forest soil

The presence of heavy metals in soils can lead to changes in microbial community structure, characterized by the dominance of groups that are able to tolerate contamination. Such groups may provide good microbial indicators of heavy-metal pollution in soil. Through terminal restriction fragment length polymorphism (T-RFLP) profiling, changes in the bacterial community structure of an acidic forest soil that had been incubated with cadmium (Cd) for 30 days were investigated. T-RFLP revealed, in particular, three operational taxonomic units (OTUs) strongly dominating in relative abundance in the contaminated soil. By cloning of the amplified 16S rRNA genes and partial sequencing of 25 clones, these three dominant OTUs were phylogenetically characterized. One dominant OTU in the cadmium-contaminated soil was derived from Betaproteobacteria, genus Burkholderia, and the other two were from uncultured members of the class Actinobacteria, closely related to the genus Streptomyces. To confirm T-RFLP data, four primers were designed on the basis of this study's dominant sequences, targeting the OTUs corresponding to Burkholderia or Actinobacteria. Real-time PCR showed that Burkholderia target sequences were more abundant in cadmium-treated soil (7.8 × 107± 3.0 × 107 targets g−1 soil) than in untreated soil (4.0 × 106± 8.9 × 105 targets g−1 soil). It was concluded that the genus Burkholderia includes species that may be particularly dominant under cadmium contaminatio

QTL analysis of seed yield components in red clover (Trifolium pratense L.)

Cultivars of red clover (Trifolium pratense L.), an important forage crop in temperate regions, are often characterised by an unsatisfactory level of seed yield, leading to high production costs. This complex trait is influenced by many components and negatively correlated with other important traits, such as forage yield or persistence. Therefore, seed yield has proven to be difficult to improve. Thus, the objectives of this study were to assess association among seed yield components and to provide the basis for identifying molecular markers linked to QTLs for seed yield components to assist breeding for improved red clover cultivars. A total of 42 SSR and 216 AFLP loci were used to construct a molecular linkage map with a total map length of 444.2 cM and an average distance between loci of 1.7 cM. A total of 38 QTLs were identified for eight seed yield components. The traits seed number per plant, seed yield per head, seed number per head, head number per plant and percent seed set were highly correlated with seed yield per plant, and QTLs for several of these traits were often detected in the same genome region. Head number per plant may present a particularly useful character for the improvement of seed yield since it can easily be determined before seed maturity. In addition, two genome regions containing four or five QTLs for different seed yield components, respectively, were identified representing candidate regions for further characterisation of QTLs. This study revealed several key components which may facilitate further improvement of seed yield. The QTLs identified represent an important first step towards marker-assisted breeding in red clover

Vergleich von Methoden zur Ermittlung der mikrobiellen Diversität in Böden des DOK-Versuches.

Die angewendeten Methoden erwiesen sich als geeignet, um die mikrobiellen Gemeinschaften und deren physiologische Eigenschaften in den Böden der Anbausysteme des DOK-Versuches zu untersuchen. Sämtliche Parameter konnten Veränderungen der physiologischen Eigenschaften und taxonomischen Zusammensetzung beschreiben, die hauptsächlich auf die unterschiedlichen Anbausysteme und Kulturen zurückzuführen sind. Es stellte sich zudem heraus, dass die Veränderungen besonders durch die Art der Düngung (organisch vs. mineralisch) hervorgerufen wurden. Die Untersuchung hat gezeigt, dass eine verknüpfende Betrachtung der Ergebnisse der hier angeführten Analysemethoden sinnvoll ist, um zukünftig verbesserte Aussagen über Bodenqualität und -fruchtbarkeit in Agrarökosystemen treffen zu können

Wirkungen von ‚Effektiven Mikroorganismen EM’ auf pflanzliche und bodenmikrobiologische Parameter im Feldversuch

The effectiveness of the bio-fertilizer ‚Effective Microorganisms’ (EM) was investigated in a four years field experiment (2003-2006) at Zürich, Switzerland. The experiment was arranged to separate the effect of the microorganisms in the EM treatments (Bokashi and EMA) from its substrate (sterilized treatments). Crop yields and soil microbiological parameters as soil respiration and microbial biomass were determined. The EM treatments showed no effect on yield and soil microbiology which were caused by the EM microorganisms. Observed effects could be related to the effect of the carrier substrate of the EM preparation. The sampling time showed stronger ef-fects on soil microbial biomass (SIR) and soil respiration compared to the effect of the treatments. Hence ‘Effective Microorganisms’ will not be able to improve yields and soil quality in mid term (3 years) in organic arable farming

Assessing potential hybridization between a hypothetical gene drive-modified Drosophila suzukii and nontarget Drosophila species.

Genetically engineered gene drives (geGD) are potentially powerful tools for suppressing or even eradicating populations of pest insects. Before living geGD insects can be released into the environment, they must pass an environmental risk assessment to ensure that their release will not cause unacceptable harm to non-targeted entities of the environment. A key research question concerns the likelihood that nontarget species will acquire the functional GD elements; such acquisition could lead to reduced abundance or loss of those species and to a disruption of the ecosystem services they provide. The main route for gene flow is through hybridization between the geGD insect strain and closely related species that co-occur in the area of release and its expected dispersal. Using the invasive spotted-wing drosophila, Drosophila suzukii, as a case study, we provide a generally applicable strategy on how a combination of interspecific hybridization experiments, behavioral observations, and molecular genetic analyses can be used to assess the potential for hybridization

Bacterial community structure and activity in different Cd-treated forest soils

In this study we compared indicators of Cd bioavailability (water extracts, Lakanen extracts, free ions) and ecotoxicity in forest soils with contrasting physico-chemical characteristics. Soil samples were treated with CdCl2 solutions (0, 0.1, 1, 10 and 100 mM) and incubated for 30 days. Microbial activity indexes (acid phosphatase, β-glucosidase, basal respiration) and changes in bacterial community structure using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting were investigated. The Cd concentrations measured ranged from 1% to 37% of the total additions in water extracts, to higher levels in Lakanen extracts. Effects of Cd were observed at bioavailable concentrations exceeding United Nations/European Economic Commission UN/ECE guidelines for total Cd in the soil solution. Basal respiration was the most affected index, while enzymatic activities showed variable responses to the Cd treatments. We also noticed that soils with pH higher than 6.7 and clay content higher than 50% showed inhibition of basal respiration but no marked shift in bacterial community structure. Soils with lower pH (pH <5.8) with less clay content (<50%) showed in addition strong changes in the bacterial community structure. Our results provide evidence for the importance of relating the effects of Cd on the soil communities to soil properties and to bioavailabilit

Genetic mapping reveals a single major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.)

Bacterial wilt caused by Xanthomonas translucens pv. graminis (Xtg) is a major disease of economically important forage crops such as ryegrasses and fescues. Targeted breeding based on seedling inoculation has resulted in cultivars with considerable levels of resistance. However, the mechanisms of inheritance of resistance are poorly understood and further breeding progress is difficult to obtain. This study aimed to assess the relevance of the seedling screening in the glasshouse for adult plant resistance in the field and to investigate genetic control of resistance to bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.). A mapping population consisting of 306 F1 individuals was established and resistance to bacterial wilt was assessed in glasshouse and field experiments. Highly correlated data (r = 0.67–0.77, P < 0.01) between trial locations demonstrated the suitability of glasshouse screens for phenotypic selection. Analysis of quantitative trait loci (QTL) based on a high density genetic linkage map consisting of 368 amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers revealed a single major QTL on linkage group (LG) 4 explaining 67% of the total phenotypic variance (Vp). In addition, a minor QTL was observed on LG 5. Field experiments confirmed the major QTL on LG 4 to explain 43% (in 2004) to 84% (in 2005) of Vp and also revealed additional minor QTLs on LG 1, LG 4 and LG 6. The identified QTLs and the closely linked markers represent important targets for marker-assisted selection of Italian ryegrass