Biology subjects

Hijri, M.

Publications and source records attributed to Hijri, M..

10 recordsLinked to original sources

bioRxiv2026

Machine Learning Identification of Functional Trait Syndromes Associated with Responsiveness to Arbuscular Mycorrhizal Fungi

Arbuscular mycorrhizal fungi (AMF) are widespread plant symbionts that enhance nutrient acquisition, growth, and stress tolerance, yet plant responsiveness to AMF varies substantially and remains difficult to predict. We developed Trait2Myco, a Random Forest based machine-learning framework that integrates plant functional traits and environmental variables to predict mycorrhizal growth response (MGR). The framework was trained using 80 observations spanning four grass species grown under four precipitation regimes. Predictor variables included leaf and root economic traits together with precipitation, while total MGR served as the response variable. A full model incorporating ten functional traits and precipitation was trained using 80% of observations and evaluated on an independent testing dataset (20%, n = 16). The full model explained 41% of variation in MGR (R2 = 0.41), whereas a reduced ecological model containing only specific leaf area, specific root area, root carbon concentration, and precipitation improved predictive performance and explained 51.7% of variation (R2 = 0.517). Ten-fold cross-validation of the full model yielded an R2 of 0.983, RMSE of 0.046, and MAE of 0.036. Variable importance analysis identified specific leaf area, precipitation, root carbon concentration, and specific root area as the strongest predictors of responsiveness. Partial dependence analysis revealed nonlinear relationships between these predictors and MGR, while principal component analysis showed that highly responsive plants occupied distinct regions of functional trait space characterized by resource-acquisitive trait syndromes. Leaf and root traits contributed nearly equally to model performance, accounting for 41.9% and 41.3% of cumulative importance, respectively, while environmental factors contributed 16.8%. An exploratory analysis using an independent AMF colonization dataset produced similarly strong predictive relationships, suggesting that trait-based machine-learning approaches may generalize across multiple AMF-associated responses. Trait2Myco provides a reproducible framework for identifying plant trait syndromes associated with responsiveness to AMF and offers a practical tool for predicting mycorrhizal benefits across environmental gradients.

ecology↗

bioRxiv2026

Rational Design of an Arid Plant-Derived Endophytic Consortium Improves Crop Performance under Controlled Conditions

Endophytic bacteria from arid medicinal plants represent a promising source of stress-adapted, plant growth-promoting (PGP) microorganisms. Here, we investigated the cultivable endophytic microbiota of Peganum harmala using both nutrient-rich and diluted media to maximize taxonomic recovery. Isolates were dominated by Bacillota and Gammaproteobacteria, with higher diversity in roots than in shoots. Venn analysis revealed a shared core fraction between compartments, forming the basis for consortium assembly. Nine representative strains belonging to Phyllobacterium, Bacillus, Brevibacillus, Burkholderia, Ralstonia, and Amycolatopsis were selected for functional screening. Pairwise antagonism assays showed high compatibility among Bacillus-related strains, whereas certain taxa exhibited inhibitory interactions, guiding rational consortium design. Functional characterization demonstrated complementary PGP traits, including nitrogen-related activity, phosphate, potassium, and silicate solubilization, siderophore and indole-3-acetic acid production, and ammonia production. No single isolate performed optimally across all traits, supporting a consortium-based strategy. A synthetic bacterial consortium (C2), reconstructed from the core endophytic microbiota using compatibility-guided selection, was evaluated in two crop systems. In vitro flax germination assays showed accelerated radicle emergence and improved vigor index, particularly with C2. Under greenhouse conditions, C2 significantly enhanced flax shoot and root biomass, root architecture, leaf area expansion, and photosystem II performance in sterile soil. In faba bean under natural soil, C2 increased leaf number (p = 0.02) relative to the control. These results indicate that consortia derived from core endophytes of arid medicinal plants can promote plant growth across diverse crops and soil contexts, although effects remain context-dependent and require rigorous field validation. IMPORTANCEEndophytic bacteria can serve as sustainable bioinoculants to enhance crop performance under stress conditions. This study demonstrates that the core microbiota of the arid medicinal plant Peganum harmala can be rationally assembled into a functionally complementary consortium that improves germination, nutrient acquisition, and whole-plant physiological performance in flax and faba bean. By combining compatibility-guided assembly with functional screening, we show that consortium-based strategies may outperform single-strain inoculants. These findings provide insight into the development of scalable, plant growth-promoting microbial consortia and highlight the importance of testing microbial inoculants under multiple environmental contexts to ensure consistent benefits.

microbiology↗

bioRxiv2026

Deterministic abiotic filtering and halophilic core microbiomes shape bacterial communities in costal salt flats (Sabkha) of southern Morocco

Coastal salt flats, locally known as Sabkhas, are hypersaline, alkaline desert ecosystems that impose extreme abiotic stress on microbial and plant life. Despite their ecological significance, plant-associated microbiomes in these habitats remain poorly characterized. In this study, we investigated the bacterial communities of native halophytes across three sabkha sites in southern Morocco using an integrated culture-independent and culture-dependent framework. Soil physicochemical analyses revealed strong gradients in salinity and ionic composition, along with consistently alkaline pH across sites. These conditions strongly structured bacterial assemblage: alpha diversity declined progressively from bulk soil to rhizosphere soil, root and shoot; and beta diversity showed clear compartmental separation driven by environmental factors. Canonical Correspondence Analysis identified electrical conductivity (EC), Na2O, K2O and carbonate fractions as the main abiotic drivers. Across plant species, bacterial communities converged toward a stable halophilic core microbiome dominated by Halomonas, Kushneria and Marinococcus, with 66% of ASVs shared across compartments. Host identity played a secondary role, as environmental filtering overshadawed host-specific associations. Culture-dependent isolation recovered 19 halophilic and halotolerant bacterial strains, mainly, Halomonas, Idiomarina, Marinobacter, Psychrobacter, Planomicrobium and Bac illus, tolerating up to 25% NaCl. The strong concordance between cultured isolates and metabarcoding profile confirms that dominant halophilic lineages are both ecologically robust and readily culturable. Together, these findings demonstrate that sabkha plant microbiomes are primarily shalped by deterministic abiotic filtering and harbor resilient, stress-adapted bacterial communities. Sabkhas thus represent promising reservoirs of halophilic microbes with potential applications in saline agriculture and improving crop resilience under extreme environmental conditions. ImportanceCoastal salt flats (sabkhas) are among the most extreme terrestrial environments, characterized by high salinity, alkalinity, and limited water availability. As soil salinization expands worldwide, understanding how life persists in such habitats is increasingly important for sustainable agriculture. This study shows that sabkha ecosystems impose strong environmental filtering on plant-associated bacterial communities, leading to highly structured microbiomes across soil, root, and shoot compartments. Despite differences among sites and plant species, bacterial communities converged toward a shared halophilic core microbiome, dominated by salt-adapted genera that are resilient to extreme ionic stress. Importantly, many of these dominant bacteria were readily culturable, highlighting sabkhas as accessible reservoirs of stress-tolerant microbes. Our findings demonstrate that abiotic conditions outweigh plant identity in shaping microbiome assembly under extreme stress and reveal sabkha halophytes as valuable natural models for discovering microbes with potential applications in saline agriculture, soil restoration, and crop resilience in salt-affected environments.

microbiology↗

bioRxiv2025

Chromosome-level phased genome assembly of the Argan tree Sideroxylon spinosum L.

Argan (Sideroxylon spinosum L. previously known as Argania spinosa) is an endemic tree of Morocco, primarily used for seed oil extraction. Increasing interest in its biology and in genes relevant for oil quality and stress resistance demands for high-quality models of its genome and transcriptome. We integrated sequencing data from PacBio HiFi long-reads and Illumina Hi-C to generate independently assembled phased genome models for both parental haplotigs with lengths of 636Mb and 655 Mb, respectively, and with a BUSCO completeness score of >97.8%. Both haplotigs consist of 11 independently assembled fully resolved telomere-to-telomere chromosomes, similar to other species of the Sapotaceae (n = 10-13), and they both contain approximately [~]60% of highly repetitive regions. Comparative analysis with other Sapotaceous genomes suggests overall chromosome conservation, with repeat expansion and chromosome fusion for the two largest chromosomes (chr1, chr2). We also independently assembled the chloroplast genome. This high-quality genome assembly provides a valuable resource for advancing future research on argan biology, its genetic diversity, and traits relevant for fitness and oil production.

genomics↗

bioRxiv2023

How does fertilization impact the wild blueberry microbiome

Wild blueberries production is regarded as less intensive than other agricultural systems, although several agricultural practices are commonly implemented to increase crop yields and to mitigate pets and pathogen attacks. Fertilization, organic or mineral, is used to increase soil nutrient availability and improve fruit yield. Wild blueberry plants are also known to depend on their microbiome to overcome the lack of nutrient availability in the soil and their symbiosis with ericoid mycorrhizal fungi is thought to be crucial in that regard. As fertilization can alter crop microbial communities, our study aimed to measure the impact of this practice in a wild blueberry setting, focusing on the bacterial and fungal communities found in the roots and rhizosphere of Vaccinium angustifolium Ait., both at the time of application and more than year later during the harvest season. Our study indicates that fertilization, whether mineral or organic, has a minimal effect on microbial communities. One year after application, fertilization does not seem to have a negative repercussion on the ericoid mycorrhizal (ErM) fungal community as no significant differences were observed in terms of relative abundance on known and putative ErM taxa between the control and the two fertilizer treatments. The fact that fertilization is applied at a low rate could explain this absence of effect on the microbial communities. However, longer-term studies are needed to ensure that repeated fertilization does not cause any shifts in microbial communities that could be detrimental to the wild blueberry nutrition. ImportanceThis study examines the impact of fertilization, whether organic or mineral, on microbial communities in the roots and rhizosphere of wild blueberry (Vaccinium angustifolium Ait.). both Fertilization is commonly used to enhance soil nutrient availability and improve fruit yield, but its effects on the plants microbiome, particularly on the ericoid mycorrhizal fungi (ErM), are not well understood. The samples were taken both during the pruning season, 3 months after the treatment, and one year later, during harvest season. The results suggest that fertilization has minimal impact on the microbial communities. One year after application, no significant differences were observed in the relative abundance of known and putative ErM taxa between the control group and the two fertilizer-treated groups. The low amount of fertilization applied could explain these results. However, longer-term research are needed to ensure that repeated fertilization does not lead to detrimental shifts in microbial communities affecting wild blueberry nutrition.

microbiology↗

bioRxiv2023

Does soil history decline in influencing the structure of bacterial communities of Brassica napus host plants across different growth stages?

Soil history has been shown to condition future plant-soil microbial communities up to a year after being established. However, previous experiments have also illustrated that mature, adult plants can "re-write", or mask, different soil histories through host plant-soil microbial community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Therefore, in this experiment we tested the hypothesis that previously established soil histories will decrease in influencing the structure of Brassica napus bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B. napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere and roots of B. napus at different growth stages-- the initial seeding conditions, seedling, rosette, bolting, and flower-- from all three soil history plots. We compared the taxonomic composition and diversity of bacterial communities, as estimated using 16S rRNA metabarcoding, to identify any changes associated with soil history and growth stages on the different B. napus soil bacterial communities. We found that soil history remained significant across each growth stage in structuring the bulk soil and rhizosphere communities, but not the roots. This suggests that the host plants capacity to "re-write" different soil histories may be quite limited as key components that constitute the soil historys identity remain present and continue to impact bacterial communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.

microbiology↗

bioRxiv2022

Soil chemistry and soil history significantly structure oomycete communities in Brassicaceae crop rotations

Oomycetes are critically important soil microbial communities, especially for agriculture where they are responsible for major declines in yields. Unfortunately, oomycetes are vastly understudied compared to bacteria and fungi. As such, our understanding of how oomycete biodiversity and community structure varies through time in the soil remains poor. Soil history established by previous crops is one factor known to structure other soil microbes, but has not been investigated for its influence on oomycetes. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae crops. We hypothesized that the previously established soil histories would structure different oomycete communities, regardless of their current Brassicaceae crop host, in both the roots and rhizosphere. We used a nested-ITS amplicon strategy incorporated with MiSeq metabarcoding, where the sequencing data was used to infer amplicon sequence variants (ASVs) of the oomycetes present in each sample. This allowed us to determine the impact of different soil histories on the structure and biodiversity of the oomycete root and rhizosphere communities from the five different Brassicaceae crops. We found that each soil history structured distinct oomycete rhizosphere communities, regardless of different Brassicaceae crop hosts, while soil chemistry structured the oomycete communities more during a dry year. Interestingly, soil history appeared specific to oomycetes, but was less influential for bacterial communities previously identified from the same samples. These results advance our understanding of how different agricultural practices and inputs can alter edaphic factors to impact future oomycete communities. Examining how different soil histories endure and impact oomycete biodiversity will help clarify how these important communities may be assembled in agricultural soils. HighlightsO_LICrop rotations model how soil history impacts subsequent microbial communities C_LIO_LIBrassicaceae oilseed crops might mitigate pathogenic oomycetes C_LIO_LISoil history significantly structures oomycete communities C_LIO_LIOomycetes are significantly affected by soil chemistry C_LIO_LIBrassicaceae crop hosts weakly influence oomycete communities C_LI O_FIG O_LINKSMALLFIG WIDTH=115 HEIGHT=200 SRC="FIGDIR/small/499733v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1f2160aorg.highwire.dtl.DTLVardef@84fbeforg.highwire.dtl.DTLVardef@b81689org.highwire.dtl.DTLVardef@1cfacf4_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

What's past is past, mostly: Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when the Brassicaceae hosts experience drought

Previous soil history and the current plant hosts are two plant-soil feedbacks that operate at different time-scales to influence the structure soil bacterial communities. In this study, we used a MiSeq metabarcoding strategy to describe the impact of five Brassicaceae host plant species, and three different soil histories, on the structure of their bacterial root and rhizosphere communities at full flower. We found that the Brassicaceae host plants were consistently significant in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed nearly the same bacterial communities, regardless of soil history. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how plant-soil feedbacks operate at different time-scales and are involved in how microbial communities are structured is a pre-requisite for employing microbiome technologies in improving agricultural systems.

plant biology↗

bioRxiv2020

SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi

In this article, we introduce a novel bioinformatics program- SeSaMe PS Function (Spore associated Symbiotic Microbes Position Specific Function) - for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi. The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure, namely amino acid usages, codon usages, and codon contexts of three codon DNA 9-mers. SeSaMe PS Function searches a query sequence against reference sequence database, identifies three codon DNA 9-mers with structural roles, and dynamically creates the comparative dataset of 54 microbial genera based on their codon usage biases. The program applies correlation Principal Component Analysis in conjunction with K-means clustering method to the comparative dataset. Three codon DNA 9-mers clustered as sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions. The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications.

bioinformatics↗

bioRxiv2020

SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi Associated Microorganisms

Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that play key roles in plant growth and soil fertility. They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores. Numerous studies have shown that diverse microorganisms live on the surface and inside their mycelia, resulting in a metagenome when whole genome sequencing (WGS) data are obtained from sequencing AMF cultivated in vivo. The metagenome contains not only the AMF sequences, but also those from associated microorganisms. In this article, we introduce a novel bioinformatics program, SeSaMe, designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing. A genus-specific usage bias database was created based on amino acid usage and codon usage of three consecutive codon DNA 9-mers encoding for an amino acid trimer in a protein secondary structure. The program distinguishes between coding sequence (CDS) and non-CDS, and classifies a query sequence into a genus group out of 54 genera used as reference. The average correct prediction percentages of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria, 65% and 73% for fungi (excluding AMF), and 49% and 72% for AMF (Rhizophagus irregularis), respectively. The program provides a means for estimating not only taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF. Therefore, the program enables users to study the symbiotic roles of associated microorganisms. SeSaMe can be applicable to other microorganisms as well as soil metagenomes. It is freely available at www.journal.com and www.fungalsesame.org.

bioinformatics↗