Biology subjects

Vestergard, M.

Publications and source records attributed to Vestergard, M..

4 recordsLinked to original sources

bioRxiv2024

Diterpenoid phytoalexins shape rice root microbiomes and their associations with root parasitic nematodes

Rice synthesizes diterpenoid phytoalexins (DPs) are known to operate in defense against foliar microbial pathogens and root-knot nematode Meloidogyne graminicola. Here, we examined the role of DPs in shaping riceassociated root microbiomes in nematode-infested rice paddy soils. Further, we assessed how DPs affect interactions between the root microbiomes and nematode communities, particularly rice root-knot nematodes from the Meloidogyne genus. We used 16S and ITS2 rRNA gene amplicon analysis to characterize the rice root-and rhizosphere-associated microbiomes of DP knock-out mutants and their wild-type parental line, at an early (17 days) and late (28 days) stage of plant development in field soil. Disruption of DP synthesis resulted in distinct composition and structure of microbial communities both relative to the parental/wild-type line but also between individual mutants, indicating specificity in DP-microbe interactions. Moreover, nematode-suppressive microbial taxa, including Streptomyces, Stenotrophomonas, Enterobacter, Massilia, and Acidibacter, negatively correlated with Meloidogyne. Comparative analysis revealed differential enrichment of microbial taxa in the roots of rice diterpenoid phytoalexin (DP) knock-out mutants versus wild-type, suggesting that DPs modulate specific taxa in the rice root microbiome. These findings indicate DPs role in plant-microbiome assembly and nematode interactions, further underscoring the potential of leveraging phytoalexins for sustainable management of crop diseases.

microbiology↗

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↗

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↗

bioRxiv2020

A novel metabarcoding strategy for studying nematode communities

Nematodes are widely abundant soil metazoa and often referred to as indicators of soil health. While recent advances in next-generation sequencing technologies have accelerated research in microbial ecology, the ecology of nematodes remains poorly elucidated, partly due to the lack of reliable and validated sequencing strategies. Objectives of the present study were (i) to compare commonly used primer sets and to identify the most suitable primer set for metabarcoding of nematodes; (ii) to establish and validate a high-throughput sequencing strategy for nematodes using Illumina paired-end sequencing. In this study, we tested four primer sets for amplicon sequencing: JB3/JB5 (mitochondrial, I3-M11 partition); SSU_04F/SSU_22R (18S rRNA, V1-V2 region); Nemf/18Sr2b (18S rRNA, V6-V8 region) from earlier studies; and MMSF/MMSR (18S rRNA, V4-V5 region), a newly developed primer set from this study. In order to test the primer sets, we used 22 samples of individual nematode species, 20 mock communities, 20 soil samples, 20 spiked soil samples (mock communities in soil), and 4 root/rhizosphere soil samples. We successfully amplified the target regions (I3-M11 partition of the COI gene; V1-V2, V4-V8 region of 18S rRNA gene) from these 86 DNA samples with the four different primer combinations and sequenced the amplicons on an Illumina MiSeq sequencing platform. We found that the MMSF/MMSR and Nemf/18Sr2b were efficient in detecting nematode compared to JB and SSU primer sets based on annotation of sequence reads at genus and in some cases at species level. Therefore, these primer sets are suggested for studies of nematode communities in agricultural environments.

ecology↗