Biology subjects

Bak, F.

Publications and source records attributed to Bak, F..

6 recordsLinked to original sources

bioRxiv2025

Synthetic bacterial community colonizes wheat roots grown in soil and mimics the assembly pattern of a field community

The root microbiome is important for plant development. The impact of the root microbiome is the sum of multiple complex interactions among microorganisms, the plant and the environment. This complexity can be reduced by designing synthetic bacterial communities (SynComs) consisting of bacteria isolated from the roots, making it possible to study these interactions. However, the translational power from SynCom experiments to explain field observations is still very low, which demonstrates the need for development of SynComs that colonize plants comparable to what is observed in the field. Hence, we developed a SynCom consisting of 13 different strains from 13 genera with varying phenotypes originating from the roots of winter wheat (Triticum aestivum cv. Sheriff). The SynCom was inoculated into gamma-irradiated soil prior to sowing and community assembly was determined over 4 weeks using 16S rRNA amplicon sequencing. The SynCom supported growth of winter wheat over a 4-week period and developed in a comparable manner to a more diverse natural community (NatCom) obtained from a soil solution. Furthermore, the temporal dynamics of the majority of the SynCom strains mimicked the development in relative abundance of their respective genera in field grown winter wheat of similar cultivar. However, this could not be translated to a different cultivar (Herup). Our results demonstrate how SynComs inoculated into gamma-irradiated soil can provide a framework for bridging the gap between greenhouse and lab experiments and field observations. At the same time it highlights the plant-genotype specific impact on community assembly.

microbiology↗

bioRxiv2025

Wheat responds to lack of root hairs with recruitment of bacteria harboring P mineralization genes and increased arbuscular mycorrhizal fungi arbuscularisation

Understanding how crops recruit bacterial and fungal partners for phosphorus (P) nutrition remains incomplete, particularly regarding temporal shifts between P-cycling bacteria and arbuscular mycorrhizal fungi (AMF). We investigated these dynamics using the wheat root hair mutant short root hair 1 (srh1), which is impaired in root hair elongation and may be more dependent on microbial P acquisition compared to the wildtype. We profiled the P-cycling bacterial microbiome and AMF colonization across development and at booting under P-depleted conditions. Before AMF establishment, the root hair mutant rhizosphere was enriched in bacterial organic P-mineralization genes. After AMF colonization increased in both genotypes, this enrichment disappeared, indicating a temporal shift from bacterial to fungal P acquisition. Growing the root hair mutant in P-depleted conditions to booting, when P uptake is highest in wheat, did not induce the mutant to recruit its bacterial P-cycling microbiome. Instead, AMF arbuscule formation was enriched. Collectively, our results reveal a temporal transition in wheat from bacterial to AMF-mediated P nutrition and highlight the compensatory role of the microbiome in plants lacking root hair elongation.

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

Viscosin synthesis influence Pseudomonas fluorescens SBW25 colonization and microbial assembly at the wheat rhizoplane in response to plant genotype

Microorganisms interact with plant roots through colonization of the root surface i.e. the rhizoplane or the surrounding soil i.e. the rhizosphere. Beneficial rhizosphere bacteria such as Pseudomonas spp. can promote plant growth and protect against pathogens by producing a range of bioactive compounds, including specialized metabolites like cyclic lipopeptides (CLPs) known for their biosurfactant and antimicrobial activities. However, the role of CLPs in natural soil systems during bacteria-plant interactions is underexplored. Here, Pseudomonas fluorescens SBW25, producing the CLP viscosin, was used to study the impact of viscosin on bacterial root colonization and microbiome assembly in two cultivars of winter wheat (Heerup and Sheriff). We inoculated germinated wheat seeds with SBW25 wild-type or a viscosin-deficient mutant, and grew the plants in agricultural soil. After two weeks, enhanced root colonization of SBW25 wild-type compared to the viscosin-deficient mutant was observed, while no differences were observed between wheat cultivars. In contrast, the impact on root-associated microbial community structure was plant genotype specific, and SBW25 wild-type specifically reduced the relative abundance of an unclassified oomycete and Phytophthora in Sheriff and Heerup, respectively. This study provides new insights into the natural role of viscosin and specifically highlights the importance of viscosin in wheat root colonization under natural soil conditions and in shaping the root microbial communities associated with different wheat cultivars. Further, it pinpoints the significance of microbial microdiversity, plant genotype and microbe-microbe interactions when studying colonization of plant roots.

microbiology↗

bioRxiv2021

Deep-rooted plant species recruit distinct bacterial communities in 3 m deep subsoil

Deep-rooted plants can obtain water and nutrients from the subsurface, making them more resilient to climatic changes such as drought. In addition, the deeper root network also allow the plants to recruit bacteria from a larger reservoir in the soil. These bacteria might contribute to nutrient acquisition and provide other plant beneficial traits to the plant. However, the deep rhizosphere communities compositions and their assembly dynamics are unknown. Here, we show, using three perennial crops, Kernza, lucerne and rosinweed, grown in 4 m RootTowers, that deep rhizosphere bacterial communities are plant specific, but clearly distinct from the shallow communities. We found that the diversity decreased with depth in the rhizosphere, whereas abundance of 16S rRNA gene copies did not change with depth in lucerne and rosinweed. Furthermore, we identified a subgroup (4-8%) of ASVs in the rhizosphere communities that could not be retrieved in the corresponding bulk soil communities. The abundances of genes determined by qPCR involved in N-cycling: amoA, nifH, nirK, nirS and nosZ differed significantly between plant species, suggesting differences in N content in the root exudates of the plant species. Our results suggest that colonization of the rhizosphere by bulk soil bacteria is not limited by carbon supply, but rather by dispersal. Furthermore, the abundance of N cycling genes indicate that deep rhizosphere bacteria have the potential to provide N through nitrogen fixation.

microbiology↗