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Numerous insertions of mitochondrial DNA in the genome of the northern mole vole, Ellobius talpinus
(2024)
Background
Ellobius talpinus is a subterranean rodent representing an attractive model in population ecology studies due to its highly special lifestyle and sociality. In such studies, mitochondrial DNA (mtDNA) is widely used. However, if nuclear copies of mtDNA, aka NUMTs, are present, they may co-amplify with the target mtDNA fragment, generating misleading results. The aim of this study was to determine whether NUMTs are present in E. talpinus.
Methods and results
PCR amplification of the putative mtDNA CytB-D-loop fragment using ‘universal’ primers from 56 E. talpinus samples produced multiple double peaks in 90% of the sequencing chromatograms. To reveal NUMTs, molecular cloning and sequencing of PCR products of three specimens was conducted, followed by phylogenetic analysis. The pseudogene nature of three out of the seven detected haplotypes was confirmed by their basal positions in relation to other Ellobius haplotypes in the phylogenetic tree. Additionally, ‘haplotype B’ was basal in relation to other E. talpinus haplotypes and found present in very distant sampling sites. BLASTN search revealed 195 NUMTs in the E. talpinus nuclear genome, including fragments of all four PCR amplified pseudogenes. Although the majority of the NUMTs studied were short, the entire mtDNA had copies in the nuclear genome. The most numerous NUMTs were found for rrnL, COXI, and D-loop.
Conclusions
Numerous NUMTs are present in E. talpinus and can be difficult to discriminate against mtDNA sequences. Thus, in future population or phylogenetic studies in E. talpinus, the possibility of cryptic NUMTs amplification should always be taken into account.
Lack of a shared vision has been identified as a major obstacle in transdisciplinary research involving both scientists and other stakeholders. Without a shared vision, the implementation of scientific findings is difficult. The diverse partners of collaborative research, however, imply a plurality in the valuation of nature and a need for deliberative mechanisms. If visioning processes are to do justice to local contexts, research must apply deliberative mechanisms to cover the plurality in the valuation of nature. This paper proposes a visioning approach for local communities, based on prior transdisciplinary research. This participatory workshop method invites stakeholders to approach nature conservation and livelihoods via a deliberation of desirable futures, barriers for achieving them and associated responsibilities for taking action. The paper explores this method via a case study of visioning workshops on sacred swamps in the Western Ghats (India), and their role for both freshwater swamp protection and livelihoods. The visioning exercise offered discussion opportunities facilitating conscientization, conciliation and collaboration in local bottom-up nature conservation. For conserving the tropical freshwater swamps, the results show the need for a more participatory forest governance, providing space for shared value creation. They also point to the need for further research on inter-faith nature conservation possibilities, along with innovations on value addition and value chain development for livelihood promotion and protection.
The cultivation of common reed (Phragmites australis) is one of the most promising practices of paludiculture on fen peatlands. This highly productive grass has a high adaptation capacity via high levels of genetic diversity and phenotypic plasticity. In this study, a reed experimental site established on a degraded fen in 1996/97 with a mixture of monoclonally (meristematically propagated plantlets) and polyclonally (pre-grown seedlings) planted plots was investigated by microsatellite genotyping. All nine genotypes of the monoclonal planted plots were recovered and could be genetically characterized; invasion by other genotypes was negligible. Similarly, the polyclonal plots sustained high clonal diversity with no prevalence of a single genotype. The growth characteristics of the five quantitatively investigated genotypes significantly differed from each other (α = 0.05): dry biomass per stem 5–18 g, panicles per m2 20–60, average stem diameter 3.5–6 mm, height 170–250 cm. Similarly, the persistence of genotypes at the planted plots and their invasiveness (ability to invade neighboured plots) varied. These results show that common reed stands are extremely persistent even if established with genotypes that are likely not to be locally adapted. Their genetic structure remained stable for at least 24 years regardless of the planting density (1, 4, and 10 plants per m2). Our results indicate that farmers may be able to maintain favourable genotypes for many years, thus the selection and breeding of common reed as a versatile crop for rewetted peatlands is a promising objective for paludiculture research.
Facing climate change, the development of innovative agricultural technologies securing food production becomes increasingly important. Plasma-treated water (PTW) might be a promising tool to enhance drought stress tolerance in plants. Knowledge about the effects of PTW on the physiology of plants, especially on their antioxidative system on a long-term scale, is still scarce. In this work, PTW was applied to barley leaves (Hordeum vulgare cv. Kosmos) and various constituents of the plants’ antioxidative system were analyzed 30 days after treatment. An additional drought stress was performed after foliar PTW application followed by a recovery period to elucidate whether PTW treatment improved stress tolerance. Upon PTW treatment, the Total Antioxidant Capacity (TAC) in leaves and roots was lower in comparison to deionized water treated plants. In contrast, PTW treatment caused a higher content of chlorophyll, quantum yield and total ascorbate content in leaves compared to deionized water treated plants. After additional drought application and subsequent recovery period, an enhancement of values for TAC, contents of malondialdehyde, glutathione as well as activity of ascorbate peroxidase indicated a possible upregulation of antioxidative properties in roots. Hydrogen peroxide and nitric oxide might mediate abiotic stress tolerance and are considered as key components of PTW.
In wet peatlands, plant growth conditions are largely determined by local soil conditions, leading to locally adapted vegetation. Despite that Carex species are often the prevailing vascular plant species in fen peatlands of the temperate zone, information about how these species adapt to local environmental conditions is scarce. This holds true especially for below-ground plant traits and for adaptations to fen-typical nutrient level variations. To address this research gap, we investigated how different geographic origins (Germany, Poland, The Netherlands) of C. acutiformis and C. rostrata relate to their response to varying nutrient availability. We performed a common garden experiment with a controlled gradient of nutrient levels, and analyzed above- and below-ground biomass production of both Carex species from the different geographic origins. We related these traits to environmental conditions of the origins as characterized by vegetation composition-derived indicator values for ecological habitat conditions. While we detected high above-ground phenotypic plasticity of Carex from different origins, our data point to below-ground genotypic differences, potentially indicating local adaptation: Rhizome traits of C. rostrata differed significantly between origins with different nutrient indicator values. These results point towards differences in C. rostrata clonal spread behavior depending on local peatland conditions. Therefore, local adaptations of plant species and below-ground biomass traits should be taken into account when studying peatland vegetation ecology, as key functional traits can differ between genotypes within a single species depending on local conditions.
Peatlands in the European Union are largely drained for agriculture and emit 25% of the total agricultural greenhouse gas emissions. Drainage-based peatland use has also negative impacts on water quality, drinking water provision and biodiversity. Consequently, key EU environmental policy objectives include the rewetting of all drained peatlands as an essential nature-based solution. Rewetting of peatlands can be combined with site-adapted land use, so-called paludiculture. Paludiculture produces biomass from wet and rewetted peatlands under conditions that maintain the peat body, facilitate peat accumulation and can provide many of the ecosystem services associated with natural, undrained peatlands. The biomass can be used for a wide range of traditional and innovative food, feed, fibre and fuel products. Based on examples in Germany, we have analysed emerging paludiculture options for temperate Europe with respect to greenhouse gas fluxes, biodiversity and indicative business economics. Best estimates of site emission factors vary between 0 and 8 t CO2eq ha−1 y−1. Suitability maps for four peatland-rich federal states (76% of total German peatland area) indicate that most of the drained, agriculturally used peatland area could be used for paludiculture, about one-third of the fen area for any paludiculture type. Fen-specific biodiversity benefits from rewetting and paludiculture, if compared to the drained state. Under favourable conditions, paludiculture can be economically viable, but costs and revenues vary considerably. Key recommendations for large-scale implementation are providing planning security by paludiculture spatial planning, establishing best practice sites and strengthening research into crops, water tables and management options.
Due to climate change, economically important crop plants will encounter flooding periods causing hypoxic stress more frequently. this may lead to reduced yields and endanger food security. As roots are the first organ to be affected by hypoxia, the ability to sense and respond to hypoxic stress is crucial. At the molecular level, therefore, fine-tuning the regulation of gene expression in the root is essential for hypoxia tolerance. Using an RnA-Seq approach, we investigated transcriptome modulation in tomato roots of the cultivar ‘Moneymaker’, in response to short- (6 h) and long-term (48 h) hypoxia. Hypoxia duration appeared to have a significant impact on gene expression such that the roots of five weeks old tomato plants showed a distinct time-dependent transcriptome response. We observed expression changes in 267 and 1421 genes under short- and long-term hypoxia, respectively. Among these, 243 genes experienced changed expression at both time points. We identified tomato genes with a potential role in aerenchyma formation which facilitates oxygen transport and may act as an escape mechanism enabling hypoxia tolerance. Moreover, we identified differentially regulated genes related to carbon and amino acid metabolism and redox homeostasis. Of particular interest were the differentially regulated transcription factors, which act as master regulators of downstream target genes involved in responses to short and/or long-term hypoxia. Our data suggest a temporal metabolic and anatomic adjustment to hypoxia in tomato root which requires further investigation. We propose that the regulated genes identified in this study are good candidates for further studies regarding hypoxia tolerance in tomato or other crops