Biology subjects

Ekelund, F.

Publications and source records attributed to Ekelund, F..

4 recordsLinked to original sources

bioRxiv2023

Fertilizer and cultivar affect the barley rhizobiome, while domestication age only affects growth at low nutrient levels

Modern plant breeding has provided barley cultivars that produce high yields when supplied with ample amounts of mineral fertilizer. This narrow selection criterion may have reduced key traits facilitating vital microbiome-plant interactions. Here, we investigated the performance of three old and four modern barley cultivars grown at different fertilizer regimes and assessed the root microbiome composition using 16s rRNA amplicon sequencing. The objectives were to investigate: i) nutrient availability effects on nutrient uptake and biomass production and, ii) how domestication age, cultivar, and fertilizer treatment affect the root microbiome. Without fertilizer, old cultivars outperformed modern ones in terms of biomass and had higher leaf concentration of nitrogen, potassium, sulphur, iron, zinc, and copper. This suggests that older barley cultivars retained the ability of their wild ancestor to collaborate with the soil microbiome resulting in improved nutrient acquisition in low-input systems. Interestingly, domestication age did not significantly affect the diversity of the rhizo-microbiome, which was instead dependent on individual cultivar and fertilizer treatment. HighlightOlder barley cultivars outperform the modern ones in terms of biomass at low nutrient availability. However, the rhizo-microbial diversity depended on the individual cultivar and fertilizer regime.

plant biology↗

bioRxiv2022

Abrupt permafrost thaw triggers microbial bloom and increased activity of microbial predators

Permafrost soils store a substantial part of the global soil carbon and nitrogen. However global warming causes abrupt erosion and gradual thaw, which make these stocks vulnerable to microbial decomposition into greenhouse gases. Here, we investigated the microbial response to abrupt in situ permafrost thaw. We sequenced the total RNA of a 1 m deep soil core consisting of up to 26500-year-old permafrost material from an active abrupt erosion site. We analysed the microbial community in the active layer soil, the recently thawed, and the intact permafrost and found maximum RNA:DNA ratios indicating a microbial bloom in recently thawed permafrost. Several fast-growing prokaryotic taxa dominated thawed permafrost, including Sphingobacteriales, Burkholderiales, and Nitrosomonadales. Overall, the thaw state and soil moisture consistently explained changes in community composition, with especially the permafrost community being significantly distinct from thawed soils. Predation correlated with changes in prokaryotic composition. Bacterial grazers were dominated by Myxococcales and abundant in the active layer. In contrast, protozoa, especially Cercozoa and Ciliophora, doubled in relative abundance in thawed layers. Our findings highlight the ecological importance of a rapid development of microbial blooms as well as the successive predation as biological control mechanism in abruptly thawing permafrost. One sentence summaryUsing total RNA from an up to 26500-year-old abruptly eroding permafrost site in Greenland, we described a microbial bloom and its controls, including bacterial and microeukaryotic predators. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/499897v2_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@10ab79eorg.highwire.dtl.DTLVardef@9d0146org.highwire.dtl.DTLVardef@1bec509org.highwire.dtl.DTLVardef@179f397_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Treated like dirt: Robust forensic and ecological inferences from soil eDNA after challenging sample storage

Biodiversity of soil microbiota is routinely assessed with environmental DNA-based methods, among which amplification and massive parallel sequencing of marker genes (eDNA metabarcoding) is the most common. Soil microbiota may for example be investigated in relation to biodiversity research or as a tool in forensic investigations. After sampling, the taxonomic composition of soil biotic communities may change. In order to minimize community changes after sampling, it is desirable to reduce biological activity, e.g. by freezing immediately after sampling. However, this may be impossible due to remoteness of study sites or, in forensic cases, where soil has been attached to a questioned item for protracted periods of time. Here we investigated the effect of storage duration and conditions on the assessment of the soil biota with eDNA metabarcoding. We extracted eDNA from freshly collected soil samples and again from the same samples after storage under contrasting temperature conditions. We used five different primer sets targeting bacteria, fungi, protists (cercozoans), general eukaryotes, and plants. For these groups, we quantified differences in richness, evenness and community composition. Subsequently, we tested whether we could correctly infer habitat type and original sample identity after storage using a large reference dataset. We found increased community composition differences with extended storage time and with higher storage temperature. However, for samples stored less than 28 days at a maximum of 20{degrees}C, changes were generally insignificant. Classification models could successfully assign most stored samples to their exact location of origin and correct habitat type even after weeks of storage. Even samples showing larger compositional changes generally retained the original sample as the best match (relative similarity). Our results show that for most biodiversity and forensic applications, storage of samples for days and even several weeks may not be a problem, if storage temperature does not exceed 20{degrees}C. Even after suboptimal storage conditions, significant patterns can be reproduced.

ecology↗

bioRxiv2019

Total RNA-sequencing reveals multi-level microbial community changes and functional responses to wood ash application in agricultural and forest soil

Recycling of wood ash from energy production may counteract soil acidification and return essential nutrients to soils. However, wood ash amendment affects soil physicochemical parameters that control composition and functional expression of the soil microbial community. Here, we applied Total RNA-sequencing to simultaneously assess the impact of wood ash amendment on the active soil microbial communities and the expression of functional genes from all microbial taxa. Wood ash significantly affected the taxonomic (rRNA) as well as functional (mRNA) profiles of both agricultural and forest soil. Increase in pH, electrical conductivity, dissolved organic carbon and phosphate were the most important physicochemical drivers for the observed changes. Wood ash amendment increased the relative abundance of the copiotrophic groups Chitinonophagaceae (Bacteroidetes) and Rhizobiales (Alphaproteobacteria) and resulted in higher expression of genes involved in metabolism and cell growth. Finally, Total RNA-sequencing allowed us to show that some groups of bacterial feeding protozoa increased concomitantly to the enhanced bacterial growth, which shows their pivotal role in the regulation of bacterial abundance in soil.

microbiology↗