| 1. |
- Schoch, Conrad L., et al.
(author)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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In: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Journal article (peer-reviewed)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 2. |
- Feng, Z., et al.
(author)
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Differential effects of ozone on photosynthesis of winter wheat among cultivars depend on antioxidative enzymes rather than stomatal conductance
- 2016
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697. ; 572, s. 404-411
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Journal article (peer-reviewed)abstract
- Five modern cultivars of winter wheat (Triticum aestivum L.): Yangmai16 (Y16), Yangmai 15 (Y15), Yangfumai 2 (Y2), Yannong 19 (Y19) and Jiaxing 002 (J2) were investigated to determine the impacts of elevated ozone concentration (E-O3) on photosynthesis-related parameters and the antioxidant system under fully open-air field conditions in China. The plants were exposed to E-O3 at 1.5 times the ambient ozone concentration (A-O3) from the initiation of tillering to final harvest. Pigments, gas exchange rates, chlorophyll a fluorescence, antioxidants contents, antioxidative enzyme activity and lipid oxidation were measured in three replicated plots throughout flag leaf development. Results showed that significant O3 effects on most variables were only found during the mid-grain filling stage. Across five cultivars, E-O3 significantly accelerated leaf senescence, as indicated by increased lipid oxidation as well as faster declines in pigment amounts and photosynthetic rates. The lower photosynthetic rates were mainly due to non-stomatal factors, e.g. lower maximum carboxylation capacity and electron transport rates. There were strong interactions between O3 and cultivar in photosynthetic pigments, light-saturated photosynthesis rate and chlorophyll a fluorescence with O3-sensitive (Y19, Y2 and Y15) and O3-tolerant (J2, Y16) cultivars being clearly differentiated in their responses to E-O3. E-O3 significantly influenced the antioxidative enzymes but not antioxidant contents. Significant interactions between O3 and cultivar were found in antioxidative enzymes, such as SOD and CAT, but not in stomatal conductance (gs). Therefore, it can be concluded that antioxidative enzymes rather than gs or antioxidants are responsible for the differential responses to E-O3 among cultivars. These findings provide important information for the development of accurate modeling O3 effects on crops, especially with respect to the developmental stage when O3 damage to photosynthesis becomes manifest. © 2016 Elsevier B.V.
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| 3. |
- Chen, Z, et al.
(author)
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Importance of heterotrophic nitrification and dissimilatory nitrate reduction to ammonium in a cropland soil: Evidences from a 15N tracing study to literature synthesis
- 2015
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In: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 91, s. 65-75
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Journal article (peer-reviewed)abstract
- Future climate change is predicted to influence soil moisture regime, a key factor regulating soil nitrogen (N) cycling. To elucidate how soil moisture affects gross N transformation in a cultivated black soil, a 15N tracing study was conducted at 30%, 50% and 70% water-filled pore space (WFPS). While gross mineralization rate of recalcitrant organic N (Nrec) increased from 0.56 to 2.47 mg N kg−1 d−1, the rate of labile organic N mineralization declined from 4.23 to 2.41 mg N kg−1 d−1 with a WFPS increase from 30% to 70%. Similar to total mineralization, no distinct moisture effect was found on total immobilization of ammonium, which primarily entered the Nrec pool. Nitrate (NO3−) was mainly produced via autotrophic nitrification, which was significantly stimulated by increasing WFPS. Unexpectedly, heterotrophic nitrification was observed, with the highest rate of 1.06 mg N kg−1 d−1 at 30% WFPS, contributing 31.8% to total NO3− production, and decreased with WFPS. Dissimilatory nitrate reduction to ammonium (DNRA) increased from near zero (30% WFPS) to 0.26 mg N kg−1 d−1 (70% WFPS), amounting to 16.7–92.9% of NO3− consumption. A literature synthetic analysis from global multiple ecosystems showed that the rates of heterotrophic nitrification and DNRA in test soil were comparative to the forest and grassland ecosystems, and that heterotrophic nitrification was positively correlated with precipitation, soil organic carbon (SOC) and C/N, but negatively with pH and bulk density, while DNRA showed positive relationships with precipitation, clay, SOC, C/NO3− and WFPS. We suggested that low pH and bulk density and high SOC and C/N in test soil might favor heterotrophic nitrification, and that C and NO3− availability together with anaerobic condition were crucial for DNRA. Overall, our study highlights the role of moisture in regulating gross N turnover and the importance of heterotrophic nitrification for NO3− production under low moisture and DNRA for NO3− retention under high moisture in cropland.
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