ABSTRACT Fusarium is a large and diverse genus of fungi of great agricultural and economic importance, containing many plant pathogens and mycotoxin producers. To date, high-throughput sequencing of Fusarium communities has been limited by the lack of genus-specific primers targeting regions with high discriminatory power at the species level. In the present study, we evaluated two Fusarium -specific primer pairs targeting translation elongation factor 1 (TEF1). We also present the new primer pair Fa+7/Ra+6. Mock Fusarium communities reflecting phylogenetic diversity were used to evaluate the accuracy of the primers in reflecting the relative abundance of the species. TEF1 amplicons were subjected to 454 high-throughput sequencing to characterize Fusarium communities. Field samples from soil and wheat kernels were included to test the method on more-complex material. For kernel samples, a single PCR was sufficient, while for soil samples, nested PCR was necessary. The newly developed primer pairs Fa+7/Ra+6 and Fa/Ra accurately reflected Fusarium species composition in mock DNA communities. In field samples, 47 Fusarium operational taxonomic units were identified, with the highest Fusarium diversity in soil. The Fusarium community in soil was dominated by members of the Fusarium incarnatum-Fusarium equiseti species complex, contradicting findings in previous studies. The method was successfully applied to analyze Fusarium communities in soil and plant material and can facilitate further studies of Fusarium ecology.
Abstract Organic farming is often advocated as an approach to mitigate biodiversity loss on agricultural land. The phyllosphere provides a habitat for diverse fungal communities that are important for plant health and productivity. However, it is still unknown how organic farming affects the diversity of phyllosphere fungi in major crops. We sampled wheat leaves from 22 organically and conventionally cultivated fields in Sweden, paired based on their geographical location and wheat cultivar. Fungal communities were described using amplicon sequencing and real‐time PCR . Species richness was higher on wheat leaves from organically managed fields, with a mean of 54 operational taxonomic units (OTUs) compared with 40 OTU s for conventionally managed fields. The main components of the fungal community were similar throughout the 350‐km‐long sampling area, and seven OTU s were present in all fields: Zymoseptoria , Dioszegia fristingensis , Cladosporium , Dioszegia hungarica , Cryptococcus , Ascochyta and Dioszegia . Fungal abundance was highly variable between fields, 10 3 –10 5 internal transcribed spacer copies per ng wheat DNA , but did not differ between cropping systems. Further analyses showed that weed biomass was the strongest explanatory variable for fungal community composition and OTU richness. These findings help provide a more comprehensive understanding of the effect of organic farming on the diversity of organism groups in different habitats within the agroecosystem.
There is an increasing interest in the use of cover crops in agriculture, in Sweden mainly for the use as catch crops to reduce nitrogen leakage. Some of these crops are known for their allelopathic abilities, which may play a role in the control of weeds and contribute to reduced herbicide use. This study aimed to explore the possible suppressive effect of the cover crop species white mustard, fodder radish, rye, and annual ryegrass on the early growth of the weed species silky windgrass, shepherd's-purse, and scentless false mayweed. In a greenhouse experiment using fresh cover crop residues, white mustard was the only crop that showed an effect. It reduced both seedling establishment, by 51 to 73%, and biomass, by 59 to 86%, of shepherd's-purse and scentless false mayweed. In contrast, in a growth chamber experiment using frozen material, mean germination time of silky windgrass was extended by 20 to 66% by all cover crops. Also, three out of four cover crops reduced root growth in scentless false mayweed by 40 to 46%, and two out of four cover crops reduced root growth in shepherd's-purse by 13 to 61%. However, considering seedling survival, white mustard was the most prominent cover crop, reducing survival by 21 to 57% in shepherd's-purse and scentless false mayweed. In this paper we provide evidence that different weed species show different response to different cover crops under climatic conditions prevailing in Scandinavia. Such results emphasize the importance of understanding weed–cover crop interactions as necessary for developing cropping systems that can utilize cover crops to suppress local weed flora.
The identification of processes governing genetic structure at different spatial scales remains a major challenge in evolutionary biology and is of considerable applied interest in conservation biology. In Euphrasia stricta five varieties have been identified (brevipila, gotlandica, stricta, suecica and tenuis) based on differences in habitat, phenology and morphology. In this thesis, I examined genetic variation at AFLP and microsatellite marker loci in relation to variation in habitat and morphology within and among varieties of E. stricta on the island Gotland in the Baltic Sea. The results are discussed in relation to evolutionary processes acting within this species complex. In a study conducted at the regional scale, the two early-flowering varieties suecica and tenuis each formed a genetically distinct group, while the three late-flowering varieties brevipila, gotlandica and stricta formed a third group. The results suggest that suecica and tenuis have ancient origins since they are genetically different both from the brevipila/gotlandica/stricta group and from each other despite their similar habitat preferences. This pattern was obtained using both marker systems. Discrepancies between AFLP and microsatellites were found in patterns of isolation by distance and in estimates of expected heterozygosity, He.Focusing on the mixed genetic group brevipila/gotlandica/stricta and the causes behind their clustering together despite differences in morphology and habitat preferences, I performed a study at a smaller geographic scale. Studying a population of E. stricta I found that, although gene flow within the population was strong, it had not prevented the formation of genetic groups associated with micro-habitat properties. An important result for conservation of the rare variety suecica is its distinct genetic separation from variety tenuis. If the aim of conservation is to preserve the uniqueness of suecica, the two varieties should be treated as separated entities.
Genetic differentiation between and within five varieties of Euphrasia stricta (var. brevipila , var. gotlandica , var. stricta , var. suecica and var. tenuis ) on Gotland was investigated, using amplified fragment length polymorphism, AFLP. The varieties are described in the literature by morphology and association to habitat type. We wanted to investigate whether the varieties are locally adapted populations to the typical habitat type for each variety or if they are preadapted to certain habitat types and have colonized Gotland in their present form. A constrained principal coordinate analysis revealed three genetically differentiated subunits within the species. The two early‐flowering varieties suecica and tenuis each formed a distinct group, while the three late‐flowering varieties brevipila, gotlandica and stricta together formed the third group. A phylogenetic tree confirms the partitioning into three groups. Within the group containing the late‐flowering varieties there are populations that pair as each other's closest relatives, but belong to different varieties. These pairs are also geographically adjacent. The phylogenetic tree had a “star‐like” appearance indicating a stronger divergence between populations than between varieties. The same pattern was seen in the partitioning of genetic diversity, with a lower amount of genetic variation occurring between varieties, F ST =0.14, than between populations within the varieties, F ST ranging from 0.26 to 0.60. In Euphrasia stricta the varieties suecica and tenuis and the group containing the varieties stricta/gotlandica/brevipila are likely to have a phylogeographical history outside Gotland, or an ancient and concealed local origin on the island. Within the group stricta/gotlandica/brevipila local evolutionary events seem to determine the variety identity, probably through local adaptation.
Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6–43.1 MB, with 13217–13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.
