Biology subjects

Nicolaisen, M.

Publications and source records attributed to Nicolaisen, M..

8 recordsLinked to original sources

bioRxiv2026

Phytoplasma mediated transcriptional changes in poinsettia buds suggest MAF3 and bZIP67 transcription factors as potential suppressors of shoot branching

O_LIShoot branching is critical not only in breeding for yield but also for ornamentals architecture. In the ornamental plant poinsettia (Euphorbia pulcherrima), shoot branching has traditionally been induced by phytoplasma (Candidatus Phytoplasma pruni) inoculation. This study aimed to identify regulatory genes that could be leveraged in future breeding-by-genetic engineering efforts to develop phytoplasma-free, branching poinsettia plants. C_LIO_LITo elucidate mechanisms of phytoplasma-induced shoot branching, we performed RNA-sequencing and assembled an axillary bud-specific transcriptome for expression analyses in phytoplasma-infected and -free poinsettia. Phenotyping and RNA-sequencing were also conducted on Arabidopsis mutants and wild-type lines to investigate the transcriptional regulatory effects of candidate genes. C_LIO_LIThe transcription factors EpMAF3 and EpbZIP67 were highly de-regulated in phytoplasma-infected poinsettia. We also found a two-fold increase in primary-stem branching levels of the Arabidopsis maf3 and bzip67 mutants, suggesting the two transcription factors as potential shoot branching suppressors. AtTcp1, a CYC-clade TCP transcription factor, was up-regulated (78x) in leaves of the maf3 mutants. Analyzing previously reported protein-level interactions for the differentially expressed genes (e.g., AtClamt, AtGh3.9/3.15, AtSaur32/36, AtAbi3, AtGamt2, AtTcp3, and AtDwf4) in bzip67 mutants shed light on other shoot branching regulators such as TCPs, PINs, ABIs, DWARF14, and BES1, highlighting two regulatory sub-networks including membrane transport and hormonal signaling. C_LIO_LIThe results open the way to rational engineering of shoot branching in poinsettia by targeted mutagenesis of MAF3 and bZIP67. In that way, the tedious and viral-infection prone process of phytoplasma inoculation can be avoided and poinsettia plants would have more homogenous branching. C_LI One-sentence summaryPhytoplasma infection in poinsettia induces bud-specific repression of the transcription factors EpMaf3 and EpbZip67, consistent with the enhanced stem branching observed in Arabidopsis maf3 and bzip67 mutant lines.

Plant Biology↗

bioRxiv2026

A Savory-based Formulation for Sustainable Management of Early Blight caused by Alternaria solani and Preservation of Tomato Fruit Quality

Environmental degradation caused by excessive chemical inputs is a major global challenge, highlighting the urgent need for sustainable agricultural solutions. Early blight of tomato (Solanum lycopersicum L.), caused by Alternaria solani, is a widespread disease with limited eco-friendly control options. This study evaluated three savory-based formulations; CC2020, CCP40, and CCE40 each containing savory essential oil with different compositions for managing early blight under both in vitro and greenhouse conditions. Among them, CC2020 demonstrated the highest efficacy in reducing disease severity and showed consistent performance under greenhouse conditions. Additionally, CC2020 helped preserve vitamin C content in tomato fruits and reduced melanin concentration in A. solani, suggesting a potential dual role in disease suppression and fruit quality maintenance. These findings suggest that CC2020 could serve as a promising, biocompatible formulation for sustainable management of tomato early blight.

plant biology↗

bioRxiv2025

Degradation of biopesticidal triterpenoid saponins by the soil bacterium Arthrobacter sp. α-11c

BackgroundSaponins, a diverse group of glycosylated triterpenoid and steroid compounds produced by plants, exhibit potent insecticidal activity and are promising candidates for sustainable pest management. However, their potential persistence in soil raises concerns about ecological impacts, highlighting the need to understand microbial degradation rates and pathways. ResultsThis study reports the isolation of Arthrobacter sp. 11c, and its ability of fully degrading two hederagenin-based pentacyclic triterpenoid saponins: -hederin, hederacoside C, and the corresponding sapogenin hederagenin. All three compounds were fully metabolized within six hours when provided as carbon source. Fractionation experiments confirmed intracellular uptake and degradation of the saponins. Genome analysis of 11c revealed diverse and multiple glycosidase genes, yet basal glucosidase activity remained unchanged when cultured with these saponins. Comparative genomics with Arthrobacter sp. 12b, a closely related strain unable to degrade saponins, revealed two unique glycosidase gene clusters in 11c, suggesting a role in adaptation to saponin metabolism. ConclusionThese findings enhance our understanding of bacterial degradation of plant triterpenoid saponins and provide a foundation for evaluating their environmental fate. This knowledge supports the safe and sustainable use of saponin-based biopesticides in agriculture by identifying microbial partners that contribute to their breakdown in soil ecosystems.

microbiology↗

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↗

bioRxiv2024

Linking microbial community structure with function using functional amplicon sequencing of the NRPS genes around wheat roots during drought stress

Secondary metabolites are bioactive compounds, diverse in structure with versatile ecological functions including key roles in mediating interactions between microorganisms and plants. Importantly, these compounds can promote the colonization of plant surfaces, such as roots, or modulate root exudates to enhance microbial recruitment and establishment. However, owing to the vast diversity of secondary metabolites, their importance in plant root colonization and in particular under stress conditions such as drought, remains unclear. To determine the involvement in root colonization of some of these secondary metabolites, we used amplicon sequencing targeting the adenylation domain of the NRPSs and the 16S rRNA gene from the rhizoplane of wheat grown in soil under normal and drought stress conditions. Results showed that drought transiently affected the bacterial community composition and the NRPS composition in the rhizoplane. We observed that drought selected for distinct groups of siderophores from different taxonomical groups, enriching for Streptomyces and depleting Pseudomonas siderophores. In addition, drought enriched Pseudomonas-derived NRPS genes encoding viscosin, a cyclic lipopeptide with biosurfactant properties, indicating that compounds linked to motility and colonization provide a competitive advantage during rhizoplane colonization under drought stress condition. This observation was experimentally confirmed using the viscosin producing P. fluorescens SBW25 and its viscosin-deficient mutant. A higher abundance of SBW25 colonized the roots under drought stress conditions compared to the viscosin-deficient mutant. In summary, our work demonstrates the potential for amplicon sequencing of NRPS genes coupled with in planta experiments to elucidate the importance of secondary metabolites in root colonization. ImportanceTo harness beneficial plant-microbe interactions for improved plant resilience, we need to advance our understanding of key factors required for successful root colonization. Bacterial produced secondary metabolites are important in plant-microbe interactions, and thus, targeting these genes generate new knowledge that is essential for leveraging bacteria for sustainable agriculture. We used amplicon sequencing of the NRPS A domain on the rhizoplane of wheat exposed to drought stress to identify important secondary metabolites in plant-microbe interactions during drought. We show that the siderophores respond differently to drought stress depending on taxonomic affiliation and that the potential to synthesize viscosin increases root colonization. Importantly, this study demonstrates the potential of amplicon sequencing of NRPS genes to reveal specific secondary metabolites involved in root colonization, particularly in relation to drought stress, and highlights how the resolution provided by this approach can link specific compounds to a specific stress condition in a soil system.

microbiology↗

bioRxiv2024

Pseudomonas taxonomic and functional microdiversity in the wheat rhizosphere is cultivar-dependent and links to disease resistance profile and root diameter

Diversity within lower taxonomic units in microbial communities is a key trait, giving rise to important ecological functions. In the rhizosphere, these functions include disease suppression and pathogen inhibition. However, limited effort has been given to exploring intragenus microdiversity in an increasingly homogenous agricultural system. Through an integrative approach combining culture-dependent and -independent methods, we explore the rhizosphere Pseudomonas pangenome and demonstrate cultivar-dependent taxonomic and functional microdiversity between two closely related modern winter wheat cultivars. A Fusarium-resistant cultivar demonstrated increased Pseudomonas taxonomic diversity but not biosynthetic diversity when compared to the susceptible cultivar, coinciding with a thinner root diameter of the resistant cultivar. We found enrichment of Pseudomonas isolates capable of antagonizing Fusarium as well as chitinase-encoding genes and pyoverdine gene clusters in the resistant cultivar. Across closely related Pseudomonas isolates from the two cultures, there were differences in genomic content and biosynthetic gene clusters. Ultimately, we highlight the need for fine-scale analysis to uncover the hidden microdiversity within rhizosphere Pseudomonas.

microbiology↗

bioRxiv2023

SNP Allocation For Estimating Heritability (SAFE-h2): A tool to explore genomic origins of phenotypes for estimation of SNP heritability using additive-only allelic effects or additive and non-additive allelic effects

Polygenicity requires the inclusion of all SNPs to ensure accurate estimation of SNP heritability. However, SNPs with large association p-values should be excluded, as they impose biologically meaningless negative contributions, i.e., downward bias, to heritability estimates. This is demonstrated with simulated data and validated using real-world datasets. We introduce SAFE-h2 as a solution to this dilemma. SAFE-h2 performs heritability profiling and establishes a p-value threshold to filter out SNPs with negative contributions. By examining 74 phenotypes across eight species, SAFE-h2 revealed an average negative contribution of 30 units, imposed by SNPs from the upper-bounds of p-value thresholds. SAFE-h2 also provides a safe p-value interval to minimize false-positive SNP hits and facilitates capturing intra-locus (Ref -alleleSNPi x Ref -alleleSNPi, Ref - alleleSNPi x Alt -alleleSNPi, and Alt -alleleSNPi x Alt -alleleSNPi) additive and non-additive effects within the framework of linear models. The allelic adjustment algorithm of SAFE-h2 revealed considerable uncaptured phenotypic variance when relying on additive effects and improved the SNP heritability estimations by up to 56 units across 50 phenotypes in six species through the combined capture of both additive and non-additive allelic effects.

bioinformatics↗

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↗