Biology subjects

Azarbad, H.

Publications and source records attributed to Azarbad, H..

13 recordsLinked to original sources

bioRxiv2026

Farming and climate legacies shape the seed microbiota and offspring drought responses in wheat

Seeds link parental environments to offspring establishment, but whether seed-associated bacteria retain signatures of farming and climate legacies across plant generations remains unclear. Here, we characterized epiphytic and endophytic bacterial communities of winter wheat seeds collected from the Global Change Experimental Facility (GCEF) in Germany across three harvest years representing contrasting climates. We then tested how farming (organic versus conventional) and climate (ambient versus future) legacies experienced by maternal plants were associated with offspring rhizosphere bacterial communities and plant performance under drought in the greenhouse. Harvest year was the dominant driver of grain dry weight and seed-associated bacterial communities. Climate legacy additionally affected seed epiphytic communities, whereas farming legacy was expressed in the endophytic diversity. Germination was higher overall for seeds from the conventional than the organic farming legacy and from the ambient than the future climate legacy. A small subset of unique seed-associated ASVs was detected in offspring rhizospheres. Although these ASVs occurred at low relative abundance in seeds (<1%), they accounted for up to approximately 40% of rhizosphere relative abundance under drought. Together, these findings show that seeds retain bacterial signatures of parental farming and climate legacies and that a subset of seed-associated ASVs remains detectable and can become abundant in offspring rhizospheres under drought.

microbiology↗

bioRxiv2026

Intra-individual variation in leaf microbiota matches within-crown environmental heterogeneity and promotes tree performance

Plant-associated microbial communities exhibit pronounced specificity across biological and spatial scales. While the patterns and accompanied functions have been well documented across and within plant species, the functional importance of intra-individual variation remains underexplored. Particularly in trees that experience strong environmental gradients within single crowns, stratum-specific microbiota may significantly contribute to plant performance. We experimentally tested whether variation in microbiota within the crown of Quercus robur is related to host performance. In mesocosm experiments, we transferred microbial communities derived from sun and shade leaves to germ-reduced clonal individuals of the same species and applied UV radiation simulating conditions that matched or mismatched the origin of the microbial inoculum (environmental matching). Our results demonstrate that matching microbiota-environment combinations increased plant performance compared to mismatching combinations. We infer that pronounced intra-individual variation of leaf-associated microbial communities not only reflects environmental heterogeneity along canopy strata but is functionally relevant for the plant host.

ecology↗

bioRxiv2026

Differential drought sensitivity of total and active wheat rhizosphere microbiome during rainfall reduction

Root-associated microorganisms play a pivotal role in helping plants adapt to drought stress. However, the underlying mechanisms of the rhizospheric microbiome under limiting soil moisture remain largely unresolved. Integrating total and active microbiome analyses enables a more accurate interpretation of microbial responses to climate change-associated water stress. We assessed the effect of reduced rainfall on two wheat genotypes, drought-tolerant (DT) and drought-sensitive (DS), using rainout shelters that allowed 100%, 75%, 50%, and 25% of natural precipitation to reach the crop. At the peak of the growing season, rhizosphere samples were collected for metagenomic (MG) and metatranscriptome (MT) sequencing. In parallel, rhizosphere volatile organic compounds (VOCs) were collected and analysed. Differential expression analysis of metatranscriptomic data using metagenomic abundance as a cofactor was performed by comparing all treatments to the 100% precipitation control. Our results demonstrate that particularly oxidative stress-related transcripts intensify in DS as rainfall decreases. Transcriptomic shifts primarily involved upregulation of transcripts associated with antioxidant (catalase, superoxide dismutase), heat shock proteins (Hsp10, Hsp60, DnaK/DnaJ, GroEL, GroES), as well as microbial functions related to osmoregulation, proline and glycine betaine (PutA, PutP, OpuBB), and plant growth-promoting traits such as auxin production, phosphate solubilization. Moreover, volatile organic compound (VOC) emissions differed significantly between the control and drought treatments, with higher emissions, particularly acetates, in the DS genotype than in the DT genotype. Overall, pronounced drought-induced shifts in active microbial functions and VOC emissions indicate high sensitivity and functional plasticity of the active microbiome, whereas the total microbiome remains robust under medium drought.

microbiology↗

bioRxiv2026

Seed microbiota legacy mitigates the effect of drought in wheat

Seeds carry epiphytes and endophytes microbial partners that can shape plant fitness. However, whether these microbial communities serve as transgenerational memory systems of parental stress remains largely unstudied. Here, we combined multi-year field rainfall manipulation experiments in eastern Canada with a greenhouse experiment in western Canada to test whether seed-associated microbiota transmit drought legacies across plant generations. In the field experiment, reduced rainfall initially decreased yield in the drought-sensitive wheat cultivar (AC Nass), but selected for distinct seed bacterial endophyte communities. In subsequent generations, plants whose seed microbiota retained compositional similarity to these drought-adapted communities showed enhanced yield stability under upcoming water stress. A transgenerational field test confirmed that daughter plants derived from drought-exposed parent plants maintained performance under water limitation, whereas those from wetter origins did not. In an independent greenhouse assay using seeds from Saskatchewan fields differing in long- and short-term irrigation history, AC Nass plants from water-stress legacy sites exhibited higher photosynthetic efficiency, water-use efficiency, and root bacterial diversity under drought. Together, these findings demonstrate that seed-associated microbiota act as ecological archives of stress history, transmitting drought legacies across generations in a cultivar and year-dependent manner.

microbiology↗

bioRxiv2025

Natural genetic transformation of the wheat rhizosphere microbial community through DNA inoculations

Rhizosphere microorganisms are known to be able to modify the plants ability to resist abiotic stresses. It is, however, difficult to modify microbial communities to improve plant phenotypes. Here we tested if a rhizosphere microbial community from a water-stress naive soil could be modified by adding DNA extracted from soils with a water stress history. Six-week-old wheat plants growing under low or high-water availabilities were inoculated with DNA extracted from soils with contrasting long-term histories of water availability - one continuously and the other intermittently exposed to water deficit. The fate of the inoculated DNA in the rhizosphere microbial communities was assessed by shotgun metagenomics. Putatively transferred inoculum genes were disproportionately found in the Acidobacteria and Bacteroidetes and belonged to functional category such as antibiotics, biofilm, and carboxylates metabolism, among others. These functional categories were shared by pre-inoculation laterally transferred genes in the recipient soil, highlighting their usefulness for life in soil. The "continuous" inoculum reduced the stress levels of wheat under reduced soil water content, suggesting that the natural genetic transformation of the rhizosphere community can feedback to the plant. Altogether, we are providing evidence for an ecological mechanism that could be harnessed to modify plant-associated microbial communities and help plants sustain water stress.

microbiology↗

bioRxiv2025

Soil microbial legacies and cultivar compatibility modulate the responses of wheat to drought

Global climate change stressors are altering soil function and reducing crop yields, yet the role of soil microbial legacies in shaping plant stress responses remains poorly understood. Here, we tested how long-term farming (organic vs conventional) and climate (ambient vs future) histories of soil microbiomes influence wheat performance under drought. Soil samples were collected from long-term experimental plots of the Global Change Experimental Facility (GCEF, Germany) and used to extract microbial communities, which were then used to inoculate sterilized potting soil in which two wheat cultivars, drought-sensitive Nordkap and drought-tolerant SU Fiete, were grown under controlled greenhouse drought. Our results showed that microbial inoculation enhanced germination relative to non-inoculated, with conventional-ambient microbiomes most strongly promoting emergence, while organic-future microbiomes suppressed seed germination. Under drought, aboveground fresh biomass and dry weight content diverged by interaction between cultivar and microbial legacy in such a way that Nordkap performed best with future-climate microbiomes, whereas SU Fiete benefited from ambient-climate microbiomes. The rhizosphere of plants inoculated with organic-derived microbes harbored a larger unique ASVs, with 442 bacterial and 70 fungal ASVs, compared with 381 bacterial and 48 fungal ASVs unique to conventional-derived microbes. We further showed that rhizosphere bacterial communities were influenced by complex interactions between microbial history (farming and climate), cultivar, and water stress, while fungal communities tracked only farming history, with organic legacies buffering fungal diversity under drought. Together, these results demonstrate that soil microbiomes retain the imprint of past management and climate, and that these legacies can either buffer or exacerbate plant stress responses depending on host genotype.

ecology↗

bioRxiv2024

A new tool in a toolbox: Addressing challenges in high-throughput microbiota surveys across diverse wild insects

With their significant effects on the biology of higher organisms, host-associated microbiota has attracted the research communitys attention. The rapid progress in sequencing techniques has greatly facilitated microbial community characterization. However, the most popular surveying technique, marker gene amplicon sequencing, has multiple caveats that are not often addressed satisfactorily, including the uncertainty about the identity of the surveyed wild-caught specimens, variable and sometimes very low abundance of microbes in some samples, or reagent- and cross-contamination. As a result, researchers often obtain incomplete, biased, and sometimes totally incorrect microbial community profiles. Here, we present a versatile, cost-effective, and high-throughput quantitative multi-target amplicon sequencing workflow for the characterization of host-associated microbial communities, combining laboratory and bioinformatic steps and addressing most of the known methodological issues. Optimized for the study of the microbiota of wild insects, it can be easily adapted for other sample types. Outputs include contamination-controlled data on the absolute abundance and identity of microbes present in insect samples, both at genotype- and OTU-level, as well as host barcodes alongside information on parasite infections. Using 1384 samples from Zackenberg Valley, NE Greenland, we demonstrate the potential of the workflow to study insect and symbiont diversity patterns across a large portion of a diverse natural community.

ecology↗

bioRxiv2024

Biological and experimental factors that define the effectiveness of microbial inoculation on plant traits: a meta-analysis

Bacterial and fungal microbiomes associated with plants can significantly affect the hosts phenotype. Inoculating plants with one or multiple bacterial and fungal species can affect specific plant traits, which is exploited in attempts to increase plant performance and stress tolerance by microbiome engineering. Currently, we lack a comprehensive synthesis on the generality of these effects related to different biological (e.g., plant models, plant traits, and microbial taxa) and experimental factors. In a meta-analysis, we showed that the plant trait under consideration and the microbial taxa used to inoculate plants significantly influenced the strength of the effect size. In a methodological context, experiments under sterilized conditions and short-term periods resulted in larger positive effects on plant traits than those of unsterilized and long-term experiments. Based on our results, we propose a comprehensive checklist as a reference for future research to standardize the design, implementation, and reporting of microbial inoculation studies. We recommend that future studies should exploit the full range of the precision-realism continuum involving (short-term) lab experiments with sterilized plants and single inoculants but also and more often (long-term) field or greenhouse experiments with naturally occurring microbial communities associated with the plants and inoculated consortia including both bacteria and fungi.

ecology↗

bioRxiv2023

The stress history of soil bacteria under organic farming enhances the growth of wheat seedlings

The effects of stress factors associated with climate change and agricultural management practices on microorganisms are often studied separately, and it remains to be determined how these factors impact the soil microbiome and, subsequently, plant growth characteristics. The aim of this study was to understand how the historical climate and agriculture to which soil microbes have been exposed can influence the growth characteristics of wheat seedlings and their associated bacterial communities. We collected soil from organic and conventional fields with different histories of climate conditions to extract microbes to inoculate wheat seeds. The results showed a positive interaction between conventional farming practices and an ambient climate for faster and higher germination rates. We demonstrate that soil microbial extracts from organic farming with experience of the future climate significantly enhanced above-ground biomass along with bacterial diversity in the seedlings compared to the soil from conventional farming. Our data suggest that soil microbiomes selected by organic farming with a history of future climates can positively impact the aboveground biomass of wheat seedlings and their bacterial assemblages, emphasizing the potential benefits of organic farming practices under changing climate conditions.

ecology↗

bioRxiv2023

Intermittent water stress favors microbial generalists that better help wheat under drought

Microorganisms can improve plant resistance to drought through various mechanisms such as the production of plant hormones, osmolytes, antioxidants, and exopolysaccharides. It is, however, unclear how previous exposure to water stress affects the functional capacity of the soil microbial community to help plants resist drought. We compared two soils that had either a continuous or intermittent water stress history for almost forty years. We grew wheat in these soils and subjected it to a water stress, after which we collected the rhizosphere soil and shotgun sequenced its metagenome. Wheat growing in the soil with an intermittent water stress history maintained a higher fresh biomass when subjected to water stress. Genes related to resistance to drought were more abundant in the metagenome and more prevalent, diversified, and redundant in the metagenome assembled genomes of the soil with an intermittent water stress history as compared to the soil with a continuous water stress history. We suggest that an intermittent water stress history selects for generalists that are adapted to both low and replete water contents, and that these generalists harbor a larger repertoire of genes beneficial for life under water stress.

microbiology↗

bioRxiv2022

Metatranscriptomic response of the wheat holobiont to decreasing soil water content

Crops associate with microorganisms that help their resistance to biotic. However, it is not clear how the different partners of this association react during exposure to stresses. This knowledge is needed to target the right partners when trying to adapt crops to climate change. Here, we grew wheat in the field under rainout shelters that let through 100%, 75%, 50% and 25% of the precipitation. At the peak of the growing season, we sampled plant roots and rhizosphere, and extracted and sequenced their RNA. We compared the 100% and the 25% treatments using differential abundance analysis. In the roots, most of the differentially abundant (DA) transcripts belonged to the fungi, and most were more abundant in the 25% precipitation treatment. About 10% of the DA transcripts belonged to the plant and most were less abundant in the 25% precipitation treatment. In the rhizosphere, most of the DA transcripts belonged to the bacteria and were generally more abundant in the 25% precipitation treatment. Taken together, our results show that the transcriptomic response of the wheat holobiont to decreasing precipitation levels is more intense for the fungal and bacterial partners than for the plant.

microbiology↗

bioRxiv2022

Early season soil microbiome best predicts wheat grain quality

Previous studies have shown that it is possible to accurately predict wheat grain quality and yields using microbial indicators. However, it is uncertain what the best timing for sampling is. For optimal usefulness of this modeling approach, microbial indicators from samples taken early in the season should have the best predictive power. Here, we sampled a field every two weeks across a single growing season and measured a wide array of microbial parameters (amplicon sequencing, abundance of N-cycle related functional genes, and microbial carbon usage) to find the moment when the microbial predictive power for wheat grain baking quality is highest. We found that the highest predictive power for wheat grain quality was for microbial data derived from samples taken early in the season (May-June) which coincides roughly with the seedling and tillering growth stages, that are important for wheat N nutrition. Our models based on LASSO regression also highlighted a set of microbial parameters highly coherent with our previous surveys, including alpha- and beta-diversity indices and N-cycle genes. Taken together, our results suggest that measuring microbial parameters early in the wheat growing season could help farmers better predict wheat grain quality.

microbiology↗

bioRxiv2021

Relative and quantitative rhizosphere microbiome profiling result in distinct abundance patterns

Next-generation sequencing is recognized as one of the most popular and cost-effective way of characterizing microbiome in multiple samples. However, most of the currently available amplicon sequencing approaches are inherently limited, as they are often presented based on the relative abundance of microbial taxa, which may not fully represent actual microbiome profiles. Here, we combined amplicon sequencing (16S rRNA gene for bacteria and ITS region for fungi) with real-time quantitative PCR (qPCR) to characterize the rhizosphere microbiome of wheat. We show that the increase in relative abundance of major microbial phyla does not necessarily result in an increase in abundance. One striking observation when comparing relative and quantitative abundances was a substantial increase in the abundance of almost all phyla associated with the rhizosphere of plants grown in soil with no history of water stress as compared with the rhizosphere of plants growing in soil with a history of water stress, which was in contradiction with the trends observed in the relative abundance data. Our results suggest that the estimated absolute abundance approach gives a different perspective than the relative abundance approach, providing complementary information that helps to better understand the rhizosphere microbiome.

ecology↗