Biology subjects

Nijhuis, E.

Publications and source records attributed to Nijhuis, E..

3 recordsLinked to original sources

bioRxiv2024

PIMENTA: PIpeline for MEtabarcoding through Nanopore Technology used for Authentication

DNA metabarcoding has become a cost-effective method to assess species composition of mixed samples. Developments such as advances in sequencing technology and increased species coverage of reference databases can be leveraged to gain more insights from metabarcoding experiments, given suitable tools. To this end, we introduce PIMENTA, a new pipeline that streamlines the analysis of Nanopore DNA metabarcoding sequencing data. PIMENTA consists of four phases: pre-processing, clustering per sample, reclustering of all samples, and taxonomic identification. PIMENTA expands a workflow created by Voorhuijzen-Harink et al. Multiple updates have been made, including parallelization of the analysis of multiple samples with the use of high-performance computing (HPC), implementation of a local taxonomy database, and expansion of the taxonomic results summary. Settings have been optimized to process higher quality nanopore reads, for an increased accuracy of taxonomic identification. We evaluated the pipeline with mock samples of zooplankton species, incorporating COI, 18SV4, and 18SV9 marker sequences. The performance and runtime have been benchmarked against two other existing pipelines. PIMENTA was able to quickly identify species with a high resolution and minimal misidentifications.

bioinformatics↗

bioRxiv2023

From amplicons to strains: The limitations of metabarcoding as criterium in the selection process of biocontrol strains against the pome fruit pathogen Neonectria ditissima

European canker, caused by the fungal pathogen Neonectria ditissima, causes severe economic losses in apple production and conventional control measures are not sufficiently effective. Recently, parts of the endophyte community have been suggested to play a role in the response of the host to the pathogen, potentially leading to higher resistance of apple cultivars to disease outbreaks. In addition, advances on biologically controlling the disease have been booked by the application of fungi isolated at the boundary of cankered and healthy wood tissue. In this study we sought to evaluate if and how metabarcoding analysis can support decisions on selection of biological control agents in a two-steps process: first we profiled fungal and bacterial taxa using Illumina MiSeq sequencing on branches of potted apple trees that had been inoculated with either water or a suspension of N. ditissima spores. We combined the knowledge on the metataxonomic profile with quantitative data on the N. ditissima branch colonisation (with relative abundances and absolute TaqMan qPCR concentrations) to identify taxa that show negative or positive correlations with N. ditissima DNA concentration. Secondly, we compared our fungal metataxonomic profile to the ITS amplicons of fungal isolates that had been tested for biocontrol potential in bioassays in a previous study. The aim was to possibly link fungal taxa with proven efficacy against the pathogen to the microbiome composition. The only ASVs showing a consistent negative correlation to relative and absolute N. ditissima abundance belonged to the bacterial genera Kineococcus and Hymenobacter. For fungal taxa only N. ditissima itself positively correlated to its increasing abundance, albeit only by rank and neither linearly nor beta binomially. Sequences belonging to the most promising antagonists from the study by Elena et al. (2022) could not be detected in the fungal microbiome profile at all. In addition, the combination of short reads length and high conservation within the chosen amplicon resulted in insufficient resolution to differentiate between a range of different efficacies of isolates belonging to the same genus (i.e. Aureobasidium).

microbiology↗

bioRxiv2023

Rhizoctonia solani disease suppression: addition of keratin-rich soil amendment leads to functional shifts in soil microbial communities

Promoting soil suppressiveness against soil borne pathogens could be a promising strategy to manage crop diseases. One way to increase pathogen suppression would be the addition of soil organic amendments, however the mechanism behind this effect remains unexplored. The presented study will focus on Rhizoctonia solani disease in sugar beet grown in two different soils. We aim to find how microbial communities and their molecular functions can be linked to Rhizoctonia solani disease suppression in sugar beet seedlings after soil is amended with a keratin-rich side stream from the farming industry. Amended soil samples were analyzed using shotgun metagenomics sequencing, and the disease score of plants infected with Rhizoctonia and grown in the same soil was collected. Results showed that both keratin-rich amended soils were rich in bacteria from the Flavobacteriaceae, Sphingobacteriaceae, Boseaceae, Phyllobacteriaceae, Caulobacteraceae, Oxalobacteraceae, Comamonadaceae, Rhodanobacteraceae and Steroidobacteraceae, as well as taxa from the phylum Bdellovibrionota, containing obligate predatory bacteria. The only fungal group that increased significantly was the Mortierellaceae family. Keratinases were abundant in the keratin-rich amended samples. Pfam domain enrichment analysis showed a decline in domains that could be annotated in both keratin-rich amended soils (Lisse [~]18% and Vredepeel [~]30%), showing an increase in unknown proteins. Among proteins that were enriched were those potentially involved in the production of secondary metabolites/antibiotics, proteins involved in motility, keratin-degradation, and contractile secretion system proteins (mostly type VI secretion system). These results could show that keratin-rich soil amendments can support the transformation into a disease suppressive soil by stimulating the same taxa that have been found in other disease suppressive soils. We hypothesize that these taxa are responsible for the suppression effect due to their genomic potential to produce antibiotics, secrete effectors via the contractile secretion system, and degrade oxalate, which is considered a virulence factor of R. solani, while simultaneously possessing the ability to metabolize keratin.

microbiology↗