Biology subjects

Finkel, O. M.

Publications and source records attributed to Finkel, O. M..

7 recordsLinked to original sources

bioRxiv2026

Conserved inhibitory mechanisms of root-associated bacteria towardsArabidopsis thaliana and Chlamydomonas reinhardtii

Soil bacteria colonize plants without causing visible disease, yet many suppress host growth. The prevalence and evolutionary reach of this cryptic inhibition are unknown, because phenotyping hundreds of isolates in plants is prohibitively slow. Here we use the unicellular algae Chlamydomonas reinhardtii as a scalable proxy for the green lineage. We screened 148 plant-associated bacteria on Chlamydomonas lawns. Seven of eight Chlamydomonas inhibitors also inhibited the vascular model plant Arabidopsis thaliana. In one of these dual inhibitors, Burkholderia sola MF6, transposon screening and proteomics implicated type VI secretion and tight-adherence pili, and over half the non-inhibitory mutants also failed against Arabidopsis. In the algae, infection triggers rapid deflagellation, then non-lytic regulated cell death. The algal zinc/iron transporter ZIP3 promotes inhibition, whereas the cathepsin X protease CEP12 restrains it, and ZIP3 is epistatic to CEP12. Cryptic inhibition is thus ancient and widespread, and a unicellular algae uncovers it at scale.

plant biology↗

bioRxiv2026

Nodule microbiome functions shape the performance of a wild perennial legume

Nitrogen fixing legume nodules are typically viewed as the product of a bilateral mutualism between host plants and nitrogen-fixing rhizobia, yet nodules also harbor diverse non-rhizobial endophytes whose functional significance remains poorly understood, especially in wild legumes and uncultivated soil. Here, using the wild Mediterranean shrub Calicotome villosa, we performed a soil inoculation experiment to test whether plant performance is linked to the functional composition of the nodule microbiome. Soil inocula from different natural sites produced strong differences in nodulation success, plant biomass, leaf nitrogen concentration, nitrogen fixation rate, and nodule allocation under otherwise uniform conditions. Although Bradyrhizobium dominated all nodules, species composition varied among inoculation sources, and non-rhizobial endophytes reached substantial abundance in some treatments. Functional profiles of the nodule microbiome were significantly associated with plant phenotype, with the strongest coupling observed for traits related to nodule investment. Targeted and genome-wide analyses identified trait-associated genes in both symbionts and endophytes, including genes involved in nitrogen cycling, ammonium transport, denitrification, pyrimidine degradation, sulfur assimilation, and type VI secretion systems. Several of these functions were not part of the canonical symbiosis machinery, yet were strongly associated with plant nitrogen status, biomass accumulation, or nodule mass fraction. Together, our results show that legume performance is better predicted by the collective functional composition of the nodule microbiome than by the primary symbiont alone. These findings support a broader view of nodules as multipartite microbial communities.

ecology↗

bioRxiv2025

Fast and accurate taxonomic domain assignment of short metagenomic reads using BBERT

Shotgun metagenomes from complex environments such as soil uncover vast biodiversity. Yet most short reads produced by shotgun sequencing cannot be taxonomically or functionally annotated, as they lack a sufficiently comprehensive reference, obscuring the true structure and function of microbial communities. We introduce BBERT, a nucleotide large language model optimized for short reads. Testing on a large cohort of soil metagenomes, we found that BBERT identifies bacterial sequence syntax without relying on reference databases, enabling accurate assignment of taxonomic domain, coding potential, and reading frame directly from reads as short as 100 bp. BBERT is small and fast enough to analyze metagenomes using a modest GPU and can be used to convert short metagenomic reads directly to bacterial amino acid sequences for downstream applications. BBERT also improves de-novo metagenomic assembly, reducing mismatches and gaps while accelerating runtime. Using metagenomes from wild legume nodules, we demonstrate that BBERT filtering improves bin quality while significantly accelerating de-novo assembly. By providing fast, reference-free classification of short reads, BBERT unlocks large metagenomic archives for more accurate ecological and evolutionary analyses.

bioinformatics↗

bioRxiv2022

MSP1 encodes an essential RNA-binding PPR factor required for nad1 maturation and complex I biogenesis in Arabidopsis mitochondria

SummaryMitochondria are semi-autonomous organelles that serve as hubs for aerobic energy metabolism. The biogenesis of the respiratory (OXPHOS) system relies on nuclear-encoded factors, which regulate the transcription, processing and translation of mitochondrial (mt)RNAs. These include proteins of primordial origin, as well as eukaryotic-type RNA-binding families recruited from the host genomes to function in mitogenome expression. Pentatricopeptide repeat (PPR) proteins constitute a major gene-family in angiosperms that is pivotal in many aspects of mtRNA metabolism, such as editing, splicing or stability. Here, we report the analysis of MITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1 (MSP1, At4g20090), a canonical mitochondria-localized PPR protein that is necessary for mitochondrial biogenesis and embryo-development. Functional complementation confirmed that the phenotypes result from a disruption of the MSP1 gene. As a loss-of-function allele of Arabidopsis MSP1 leads to seed abortion, we employed an embryo-rescue method for the molecular characterization of msp1 mutants. Our data show that msp1 embryo-development fails to proceed beyond the heart-torpedo transition stage as a consequence of a severe nad1 pre-RNA processing-defect, resulting in the loss of respiratory complex I (CI) activity. The maturation of nad1 involves the processing of three RNA-fragments, nad1.1, nad1.2 and nad1.3. Based on biochemical analyses and the mtRNA profiles in wild-type and msp1 plants, we concluded that through its association with a specific site in nad1.1, MSP1 facilitates the generation of its 3-terminus and stabilizes it -a prerequisite for nad1 exons a-b splicing. Our data substantiate the importance of mtRNA metabolism for the biogenesis of the respiratory machinery during early-plant development.

plant biology↗

bioRxiv2021

Identification of beneficial and detrimental bacteria that impact sorghum responses to drought using multi-scale and multi-system microbiome comparisons

BackgroundDrought is a major abiotic stress that limits agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere and may lead to enrichment of specific groups of microbes, such as Actinobacteria. How these changes ultimately affect plant health is not well understood. In parallel, model systems have been used to tease apart the specific interactions between plants and single, or small groups of microbes. However, translating this work into crop species and achieving increased crop yields within noisy field settings remains a challenge. Thus, the next scientific leap forward in microbiome research must cross the great lab-to-field divide. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key beneficial and detrimental, root associated microbes that robustly affect drought stressed plant phenotypes. ResultsFifty-three bacterial strains, originally characterized for association with Arabidopsis, were applied to sorghum seeds and their effect on root growth was monitored for seven days. Two Arthrobacter strains, members of the Actinobacteria phylum, caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, strains of Variovorax were able to protect both Arabidopsis and sorghum from the RGI caused by Arthrobacter. As a transitional system, we tested the synthetic communities through a 24-day high-throughput sorghum phenotyping assay and found that during drought stress, plants colonized by Arthrobacter were significantly smaller and had reduced leaf water content as compared to control plants. However, plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across well-watered and drought conditions. Drought responsive microbes were identified, including an enrichment in Actinobacteria, consistent with previous findings. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a newly developed method and were then able to observe that the abundance of Arthrobacter strains negatively correlated with plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of high confidence bacterial taxa that positively associated with plant growth under drought stress. ConclusionsA three-tiered experimental system connected reductionist and ecological approaches and identified beneficial and deleterious bacterial strains for sorghum under drought stress.

microbiology↗

bioRxiv2019

Root development is maintained by specific bacteria-bacteria interactions within a complex microbiome

Plants grow within a complex web of species interacting with each other and with the plant. Many of these interactions are governed by a wide repertoire of chemical signals, and the resulting chemical landscape of the rhizosphere can strongly affect root health and development. To understand how microbe-microbe interactions influence root development in Arabidopsis, we established a model system for plant-microbe-microbe-environment interactions. We inoculated seedlings with a 185-member bacterial synthetic community (SynCom), manipulated the abiotic environment, and measured bacterial colonization of the plant. This enabled classification of the SynCom into four modules of co-occurring strains. We deconstructed the SynCom based on these modules, identifying microbe-microbe interactions that determine root phenotypes. These interactions primarily involve a single bacterial genus, Variovorax, which completely reverts severe root growth inhibition (RGI) induced by a wide diversity of bacterial strains as well as by the entire 185-member community. We demonstrate that Variovorax manipulate plant hormone levels to balance this ecologically realistic root communitys effects on root development. We identify a novel auxin degradation operon in the Variovorax genome that is necessary and sufficient for RGI reversion. Therefore, metabolic signal interference shapes bacteria-plant communication networks and is essential for maintaining the roots developmental program. Optimizing the feedbacks that shape chemical interaction networks in the rhizosphere provides a promising new ecological strategy towards the development of more resilient and productive crops.

microbiology↗

bioRxiv2019

The effects of soil phosphorous content on microbiota are driven by the plant phosphate starvation response

Phosphate starvation response (PSR) in non-mycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms - the plant microbiota - are exposed to direct influence by the soils phosphorous (P) content itself, as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient, and compared the composition of their shoot and root microbiota to wild type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota composition than P concentrations in both roots and shoots. The fungal microbiota was more sensitive to P concentrations per se than bacteria, and less depended on the soil community composition.\n\nUsing a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift is accompanied by changes in microbiota composition: the genus Burkholderia is specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrate that in the absence of Burkholderia from the SynCom, plant shoots accumulate higher phosphate levels than shoots colonized with the full SynCom, only under P starvation, but not under P-replete conditions. Therefore, P-stressed plants allow colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plants P starvation.

microbiology↗