Biology subjects

Nicolaisen, M. H.

Publications and source records attributed to Nicolaisen, M. H..

7 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

Successive cultivation under drought selects for specific microbiome members in the wheat rhizosphere

Growing knowledge on plant microbiomes demonstrates the contribution of the host plant during microbiome assembly, especially under stress conditions commonly threatening crops. To dissect the influence of a plant on its microbiome, repeated cycling of microbiomes can be utilized to enhance functional properties in the enriched microbial communities. We used such a successive cultivation approach for wheat (Triticum aestivum) microbiome under drought conditions and selected lineages for drought resilience and susceptibility, with and without enriching the starting community with a wheat isolate library. Significant differences in the rhizosphere microbiome between selection regimes were confirmed through 16S rRNA gene amplicon sequencing. Notably, replicate lineages of each selection regime showed convergence to similar microbiomes. Specific genera were abundant depending on the selection regimes; Stenotrophomonas under drought resilience, while Rahnella under drought conditions when the strain library was added initially. Applying Stenotrophomonas or Rahnella as single inoculum did not improve drought resilience in wheat. We hypothesize that complex microbiome dynamics take place during successive cultivation, which underscores the importance of considering complex plant-microbiome systems for studying plant stress resilience. Successive cultivation remains a valuable approach for observing rhizosphere microbiome changes under different conditions.

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↗

bioRxiv2025

Myxobacteria isolated from RAS: Ecology and significance as off-flavor producers

Despite advances in the operation of recirculating aquaculture systems (RAS), accumulation of earthy-muddy off-flavors in the fish remains a potential risk. Myxobacteria (Myxococcota) are reported to be among the most abundant geosmin synthase-harboring groups in RAS, but previous isolation attempts have been unsuccessful, limiting the knowledge of their role in off-flavor production. For the first time, we successfully isolated two geosmin-producing myxobacteria from RAS: Myxococcus virescens AT3 and Corallococcus exiguus AT4. Cell-specific geosmin production varied with the nutrient content in different media but was highest in a low-nutrient medium and when cultivated in water from RAS. Cultivation in RAS water also stimulated the production of other volatile organic compounds (VOCs). Newly identified potential off-flavor compounds included 4-methyl-2-heptanone ("forest" odor), 3-methyl-1-butanol ("medicinal" and "chemical"), and a presumptive sesquiterpenoid described as "musty," "earthy," and "flowery." The previously known off-flavor compound dimethyl sulfide was also detected. Myxobacteria have previously been proposed as keystone bacteria in the environment due to their predatory lifestyle. In predation assays using isolated bacteria from RAS, M. virescens AT3 and C. exiguus AT4 could successfully feed on 15 of 16 tested strains, suggesting a large influence on the biology of RAS microbiomes. The combination of predatory behavior and potent production of geosmin and other VOCs underscores the ecological and sensory impact of these bacteria in RAS. Understanding their behavior and metabolic outputs is critical to developing strategies for mitigating off-flavors in RAS. IMPORTANCEIssues with off-flavored fish in recirculating aquaculture systems (RAS) due to the presence of the earthy-musty smelling compounds geosmin and 2-MIB is considered one of the industrys most economically significant challenges. Knowledge of conditions that affect off-flavor production is essential information in the development of viable solutions for its mitigation. Little is known about the function of these microbially produced compounds or the conditions that trigger their production, especially in the underexplored myxobacteria. Investigation of natural isolates is crucial to determine the function of the genes involved and their differential expression in response to environmental cues. While myxobacteria in RAS have been previously shown to harbor the geosmin synthase gene through molecular studies, the present study is the first attempt to isolate these bacteria from RAS and quantify their geosmin production under different nutrient conditions. Through cultivation-based methods, we demonstrate their production of both known and novel compounds with earthy attributes.

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↗

bioRxiv2020

A novel microcosm for recruiting inherently competitive biofertilizer-candidate microorganisms from soil environments

Fertilizer phosphorus (P) is both a necessary crop nutrient and finite resource, necessitating the development of innovative solutions for P fertilizer efficiency and recycling in agricultural systems. Myo-inositol hexakisphosphate (phytate) and its lower order derivatives constitute the majority of identified organic P in many soil types and has been shown to accumulate with increasing application of P fertilizer. Phytate is only poorly available to plants, and in alkaline soils it often precipitated as even more unavailable calcium (Ca)-phytate. Incorporating phytase-producing biofertilizers (i.e., microbial-based products with capacity to mineralize phytate) into soil presents a viable and environmentally acceptable way of utilizing P from phytate, whilst reducing the need for mineral P application. Here we present an in-soil microcosm that utilizes precipitated Ca-phytate to recruit microorganisms with degradation activity towards phytate in solum. Our results show both direct and indirect evidence for Ca-phytate mineralization in vitro and in solum. Furthermore, the abundance of bacteria recruited was measured via 16S rRNA gene copy number, as was three genes relating to organic P degradation; phoX and phoD phosphatases and the BPP ({beta}-propeller phytase) gene. Amplicon sequencing as well as BioLog catabolism studies show that microcosm treatments containing the bait Ca-phytate, recruited a different set of microorganisms when compared to controls. These Ca-phytate microcosms recruited mainly Actinobacteria, Firmicutes, and Proteobacteria, and the genus Streptomyces was specifically enriched. We conclude that our microcosm presents an innovative approach for isolating soil microorganisms with the potential to degrade precipitated phytate in solum and represents a new isolation method with the potential to isolate inherently robust biofertilizer candidates directly from target soils.

ecology↗