Biology subjects

Lutap, K.

Publications and source records attributed to Lutap, K..

4 recordsLinked to original sources

bioRxiv2025

Plant age and genotype explain variation in the microbiome of natural Lotus corniculatus populations

In natural populations, plants are associated with a huge diversity of bacteria, fungi and other microbes. There is usually substantial microbiome variation between different plant individuals and populations, and the drivers of this variation are still poorly understood, particularly in wild plants. Here, we were interested in the potential of plant genotype and plant age to explain intraspecific variation in the plant microbiome of Lotus corniculatus. In seven natural populations, we genotyped a total of 168 individuals over four years, determined their ages through growth ring analysis, and then sequenced their root, shoot, flower and seed microbiomes. We found that plant genotypes differed both in the diversity and composition of microbes, and that some microbial taxa were associated with particular plant genotypes. The genotype effects tended to be strongest and most consistent for plant-associated bacteria, with the largest plant genotype differences in the microbiome diversity of flowers and seeds. We found less evidence for an effect of plant age on microbiome diversity: the age of plants explained variation in fungi diversity, and it was associated with the abundance of several microbial taxa. Our study indicates that the genotype of a plant and - to a lesser degree its age - influences the diversity and composition of plant-associated microbiota, even in complex natural environments. ImportanceThe plant microbiome plays a key role in important plant functions such as pathogen resistance, nutrient uptake, and stress tolerance. To fully understand these processes, it is essential to identify the factors that drive microbiome variation. Most research to date has focused on model or crop species under controlled conditions, leaving open questions about the drivers of microbiome diversity and composition in natural populations. In this multi-year field study, we examined how plant genotype and age shape the microbiomes of Lotus corniculatus. We show that the plant genotype strongly influences microbial diversity and composition, while plant age has subtler but still important effects, particularly on fungal communities. To our knowledge, this is the first study to link plant age with microbiome variation in natural populations. These findings demonstrate that plant traits can shape the microbiome even in complex natural environments.

microbiology↗

bioRxiv2025

Organ-specific filtering by abiotic and biotic environmental factors shapes distinct yet overlapping microbial communities across Lotus corniculatus roots, shoots, flowers, and seeds

Plant microbiome assembly is modulated via filtering by the host plant and local environment as well as stochastic processes like microbial dispersal. Lotus corniculatus in natural populations that are continuously exposed to natural perturbations and microbial sources is an ideal plant model system to study the ecological processes that structure the distinct yet overlapping microbial communities in plant organs. We observed spatial and temporal variation in microbiomes associated with L. corniculatus roots, shoots, flowers, and seeds across seven grassland sites for four years. In this study we examined how abiotic and biotic factors in the local environment throughout multiple years contribute to the structure of microbiomes associated with L. corniculatus populations. We show that plant microbiomes are shaped by a set of environmental factors that are distinct to each plant compartment. These environmental factors either directly influence the plant microbiomes or by indirectly affecting them via other biotic factors. The environmental factors soil temperature seasonality, soil microbiome composition, air temperature seasonality, plant community richness, and grazing are found to influence the structure and microbial interactions in the plant organs, and are different in relationships with microbiomes with each compartment, possibly influencing dispersal decisions of microorganisms and consequently contribute in shaping distinct yet overlapping microbiomes across plant organs. Burkholderia and Sulfuritalea, plant-associated microbes that are highly correlated with environmental variables across all plant organs, respond to environmental variables differently depending on their organ microhabitat. This organ-dependent environmental perception is also observed in biomarker microbes in roots, shoots, and flowers, such as the rhizobial symbiont Mesorhizobium, leaf pathogen Setosphaeria, and necrotroph Botryotinia, respectively. Our knowledge about the organ-specific response of plant microbiomes to abiotic and biotic perturbations will equip us with a framework to understand and engineer plant microbiomes in the context of global climate change. The observed patterns on dispersal decisions or habitat choice based on organ-dependent environmental cues and microbial interactions in plant microbiomes also advance our insights on how beneficial microbes or pathogens survive and persist on specific plant microhabitat and environmental conditions.

microbiology↗

bioRxiv2025

Organ-specific microbiomes in natural Lotus corniculatus populations: Metacommunity dynamics in the plant endosphere

The structure of plant microbial communities vary due to a broad range of factors such as host and environmental factors, abiotic and biotic perturbations, and various assembly processes occurring at multiple tempo-spatial scales. In natural environments plant microbial communities are constantly exposed to such perturbations and processes. Thus, to attain a systemic understanding of the ecology of plant microbiomes, it is essential to study assembly processes that influence patterns of microbial community structures in natural environments. In this study we examined bacterial, fungal, and eukaryotic communities in plant organs of Lotus corniculatus in natural populations at seven grassland sites for four years. We used the framework of metacommunity theory of ecology to understand assembly processes that shape community structures and variations by defining microbial communities associated with the roots, shoots, flowers, and seeds as distinct communities linked by dispersal. In this study we show the organ-specificity of plant endophytic communities. Our findings suggest that selective filtering by plant organs, microbial interactions, as well as abiotic and biotic factors at tempo-spatial scales result in distinct core microbiomes of plant organs. In addition, transmission of microorganisms from within and outside the plant hosts accounts for the distinct yet overlapping organ microbiomes. We could provide a comprehensive knowledge of the stochastic and deterministic assembly processes that shape plant microbial communities in natural conditions. Understanding these ecological processes is essential for harnessing beneficial effects of plant-associated microbial communities on plant productivity, resilience, and pathogen defense.

microbiology↗

bioRxiv2023

Seasonality adaptation patterns of the natural Arabidopsis leaf microbiome over several plant generations are shaped by environmental factors

Leaf-associated microbial communities can promote plant health and resistance to biotic and abiotic stresses. However, the importance of environmental cues in the assembly of the leaf endo- and epi-microbiota remains elusive. Here we aimed to investigate the impact of seasonal environmental variations, on the establishment of the leaf microbiome, focusing on long-term changes (five years) in bacterial, fungal, and non-fungal eukaryotic communities colonizing the surface and endosphere of six wild Arabidopsis thaliana populations. While leaf-microbial communities were found to be highly stochastic, the leaf niche had a predominant importance with endophytic microbial communities consistently exhibiting a lower diversity and variability. Furthermore, our analyses revealed that among environmental factors, radiation and humidity-related factors are the most important drivers of diversity paderns in the leaf, albeit with stronger effects on epiphytic communities. Using linear models, we further identified 30 important genera whose relative abundance in leaf compartments could be modeled from environmental variables, suggesting specific niche preferences for these taxa. With the hypothesis that these environmental factors could impact interactions within microbial communities, we analyzed the seasonal paderns of microbial interaction networks across leaf compartments. We showed that epiphytic networks are more complex than endophytic, and that the complexity and connectivity of these networks are partially correlated with the mentioned environmental cues. Our results indicate that humidity and solar radiation function as major environmental cues shaping the phyllosphere microbiome at the micro-scale (leaf compartment) and macro-scale (site). These findings could have practical implications for selecting and developing field-adapted microbes in the face of, and for predicting microbial invasions in response to global change.

microbiology↗