Biology subjects

Almario, J.

Publications and source records attributed to Almario, J..

8 recordsLinked to original sources

bioRxiv2026

Helotiales fungi as potential nutritional partners for non-mycorrhizal plants: a machine learning and experimental approach

BackgroundMost land plants depend on the ancestral arbuscular mycorrhizal (AM) symbiosis for phosphorus (P) acquisition. However, several plant lineages have independently lost this symbiosis, raising fundamental questions about how these non-mycorrhizal plants meet their nutritional requirements without this crucial partnership. ResultsComparative genomic analyses confirmed that Cyperaceae, Caryophyllaceae, and Brassicaceae lack genes essential for AM symbiosis, indicating that these lineages independently abandoned this association 90-122 million years ago. Field surveys of 42 wild populations across seven sites revealed that while non-mycorrhizal plants generally maintain shoot P levels comparable to those in AM neighbors, lower shoot P levels can be observed in low P soils. To identify fungal taxa potentially associated with P nutrition in non-mycorrhizal plants, we applied a machine-learning approach to predict plant P-accumulation from root microbiome composition. The model explained substantial variance in plant P-accumulation (57-69%), and identified 85 fungal taxa as key predictors of shoot P-accumulation, predominantly belonging to the Helotiales (28%) and Pleosporales (23%) orders. Experimental validation of two phylogenetically distant Helotiales lineages (Tetracladium maxilliforme OTU29 and Helotiales sp. OTU7), using isotopic tracing, demonstrated their capacity to enhance plant growth and transfer P (and N) to their native non-mycorrhizal hosts under P-limiting conditions. ConclusionsOur findings suggest that non-mycorrhizal plants engage in nutritional partnerships with diverse Helotiales lineages that could collectively contribute to their mineral nutrition. However, given the widespread distribution of these Helotiales fungi, including in roots of AM plants, they may play a broader role in plant nutrition, i.e. also in mycorrhizal hosts. This study provides proof of concept for a novel framework integrating machine-learning predictions with experimental validation to identify functionally important microbial partnerships in natural plant communities.

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↗

bioRxiv2024

Needle in a haystack: culturing plant-beneficial Helotiales lineages from plant roots

Root-associated Helotiales fungi are increasingly recognized as beneficial fungal partners promoting plant growth under nutrient-limited conditions, particularly in non-mycorrhizal hosts, lacking the ancestral arbuscular mycorrhizal symbiosis. However, the ecology of these fungi is still cryptic as relatively few lineages have been successfully cultivated from roots for further study. Here, we attempted the mass isolation of root endophytic fungi to evaluate the recovery of known plant-beneficial Helotiales lineages using a tailored culture-based approach. We sampled six wild non-mycorrhizal species from the Brassicaceae, Caryophyllaceae, and Cyperaceae, growing in nutrient-limited alpine soils. We isolated 602 root endophytes and compared this culturable diversity with the one observed via fungal ITS2 metabarcoding. Metabarcoding revealed that Helotiales taxa dominated the fungal communities, with 43% of these detected taxa also represented in our collection. Accordingly, most root endophytes in our collection (53%) were Helotiales. These isolates, some with P solubilisation potential, belonged primarily to three Helotialean clades and were phylogenetically related to plant growth-promoting or mycorrhizal-like strains. This analysis highlights that roots of alpine non-mycorrhizal plants are reservoirs of plant-beneficial root-endophytic Helotiales, and the isolates obtained are a promising resource to explore the plant-beneficial mechanisms and ecological traits of these fungi.

microbiology↗

bioRxiv2024

Biotic interactions shape infection outcomes in Arabidopsis

The plant microbiome protects plants from stresses, including pathogen attacks. However, identifying microbes that provide plant protection remains challenging in complex microbial communities. In this study, we analysed samples from natural A. thaliana populations, including both plants infected with the pathogenic oomycete Albugo laibachii and uninfected plants, over six years. Using machine learning classification models, we achieved high accuracy in distinguishing infected and uninfected plants based on microbiome abundance. We identified 80 key taxa associated with health and disease. Among the health-associated microbes (HCom), we selected bacteria, fungi, and cercozoa that effectively reduced pathogen presence in co-inoculation assays. In comparison, disease-associated microbes (DCom) were less effective in conferring protection. Our findings highlight the complexity of plant-microbe interactions and advance our understanding of microbial roles in plant disease ecology. By integrating ecological insights with machine learning, we take a significant step towards designing robust microbial consortia that enhance plant resilience against pathogens.

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↗

bioRxiv2021

Life on leaves : uncovering temporal dynamics in Arabidopsis' leaf microbiota

Leaves are primarily responsible for the plants photosynthetic activity. Thus, changes in the phyllosphere microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. In this context, identifying the processes and microorganisms that drive the changes in the leaf microbiota over a plants lifetime is crucial. In this study we analyzed the temporal dynamics in the leaf microbiota of Arabidopsis thaliana, integrating both compositional changes and changes in microbe-microbe interactions via the study of microbial networks. Field-grown Arabidopsis were used to follow leaf bacterial, fungal and oomycete communities, throughout the plants growing season (extending from November to March), over three consecutive years. Our results revealed the existence of conserved time patterns, with microbial communities and networks going through a stabilization phase (decreasing diversity and variability) at the beginning of the plants growing season. Despite a high turnover in these communities, we identified 19 core taxa persisting in Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network hubs and hubs alternate with time. Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting it could be possible to predict and drive these microbial communities to desired states.

microbiology↗

bioRxiv2020

Obtaining deeper insights into microbiome diversity using a simple method to block host and non-targets in amplicon sequencing

Microbiome profiling is revolutionizing our understanding of biological mechanisms such as metaorganismal (host+microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci is an instrumental tool for characterization of the highly diverse microbiomes of natural systems. Investigations in many study systems are hindered by loss of essential sequencing depth due to amplification of non-target DNA from hosts or overabundant microorganisms. This issue requires urgent attention to address ecologically relevant problems using high throughput, high resolution microbial profiling. Here, we introduce a simple, low cost and highly flexible method using standard oligonucleotides ("blocking oligos") to block amplification of non-targets and an R package to aid in their design. They can be dropped into practically any two-step amplicon sequencing library preparation pipeline. We apply them in leaves, a system presenting exceptional challenges with host and non-target microbial amplification. Blocking oligos designed for use in eight target loci reduce undesirable amplification of host and non-target microbial DNA by up to 90%. In addition, 16S and 18S "universal" plant blocking oligos efficiently block most plant hosts, leading to increased microbial alpha diversity discovery without biasing beta diversity measurements. By blocking only chloroplast 16S amplification, we show that blocking oligos do not compromise quantitative microbial load information inherent to plant-associated amplicon sequencing data. Using these tools, we generated a near-complete survey of the Arabidopsis thaliana leaf microbiome based on diversity data from eight loci and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. The blocking oligo approach has potential to make new questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems-based insights into microbial discovery.

microbiology↗

bioRxiv2018

Arabidopsis thaliana populations support long-term maintenance and parallel expansions of related Pseudomonas pathogens

Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site survey of Pseudomonas in the natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a pathogenic clade present in all sites. Sequencing of 1,524 Pseudomonas genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically distinct pathogenic sublineages. These sublineages have expanded in parallel within the same populations and are differentiated both at the level of gene content and disease phenotype. Such coexistence of diverse sublineages indicates that in contrast to crop systems, no single strain has been able to overtake these A. thaliana populations in the recent past. Our results suggest that the selective pressures acting on a plant pathogen in wild hosts may be more complex than those in agricultural systems.

microbiology↗