Biology subjects

Couradeau, E.

Publications and source records attributed to Couradeau, E..

11 recordsLinked to original sources

bioRxiv2026

Active and total rhizosphere microbiomes of plant mixtures diverge from additive expectations, depending on nitrogen and plant composition

Mixing plant functional groups can boost plant productivity, but the underlying rhizosphere microbial dynamics remain unclear. We tested when to expect divergence from additive expectations by measuring plant traits and active and total rhizosphere microbiomes (via BONCAT-FACS and 16S rRNA gene amplicon sequencing) in monocultures and mixtures of legumes, brassicas, and grasses under varying nitrogen. While shoot biomass was predictable from monocultures, legume-containing mixtures yielded greater-than-expected root biomass and N-fixation. Each plant species supported distinct active and total microbiomes, and nitrogen addition increased microbiome divergence among plant species and their mixtures. In most plant mixtures, microbiomes were additive combinations of those associated with the individual species; legume-grass combinations were a notable exception, showing non-additive shifts in microbial composition, microbial activity, and the abundance of Rhizobium sp. This divergence from additive expectations coincided with non-additive biomass gains in legume-grass mixtures, suggesting that emergent plant-microbe interactions may underlie synergistic belowground responses.

ecology↗

bioRxiv2026

Using BONCAT-FACS to probe the active soil microbial community during nitrous oxide production

Nitrous oxide (N2O) is a potent greenhouse gas and is largely produced by incomplete denitrification. Although we know many of the microbial species that denitrify, we are still unable to reliably predict N2O production from soils. Recent work in microbial ecology has shown that when key microbes are considered as members of functional ensembles rather than isolated, the predictive power linking their activity to emergent properties increases dramatically. We hypothesized that the active microbial community during high N2O production would be taxonomically distinct from the inactive portion and increases in N2O production rates would correlate more strongly with increased abundance across multiple active taxa than with dominance by a single active species. We conducted a microcosm experiment where agricultural soil was incubated in anaerobic vials for up to 15 hours while tracking N2O production. Using bioorthogonal non-canonical amino acid tagging paired with fluorescence-activated cell sorting and 16S rRNA amplicon sequencing (BONCAT-FACS-Seq), we probed the active subset of the microbial community throughout the incubation period. Analysis of 16S rRNA gene amplicons revealed that the active and inactive fractions contained distinct taxa, and the taxonomic composition of the active fraction shifted over time. We found that less than 1% of the microbial community was responsible for N2O flux rates as high as 3.84 {micro}g N2O-N g dry soil-1 hr-1. The level of activity (median fluorescent intensity of active cells) correlated well with N2O production rates. The Ensemble Quotient Optimization for Microbiomes (mEQO) tool was used to identify an ensemble of eight organisms whose combined abundance best correlated with N2O fluxes. Overall, our results reveal that N2O fluxes are driven not by changes in a single taxon but by shifting ensembles of active microorganisms whose combined functional potential supports consistent emissions. This study applied a novel conceptual and methodological framework with a distinct focus on the active microbial community, rather than the entire community; if our observation that N2O flux rates are correlated with an ensemble of organisms is broadly confirmed, then framing denitrification as a community trait may increase predictability of this key process.

ecology↗

bioRxiv2026

Resident soil microbial diversity and urea amendment legacy interact to shape the composition and expression of a surface film-forming soil inoculant

Soil microbial inoculants have the potential to improve crop yield, enhance agricultural sustainability, and support soil restoration, but they often display unpredictable in-field performance across varied soil conditions. Cyanobacteria-dominated soil surface consortia (SSCs) offer a tractable model for studying inoculant-soil interactions because their visible surface growth enables direct observation and sampling after application. Here, we introduced the SSC "DG1," dominated by the diazotrophic cyanobacterium Nostoc linckia, into soil microcosms differing in resident microbiome diversity (low vs. high diversity) and urea fertilization history, (+urea vs. -urea). We used 16S rRNA gene sequencing and genome-resolved metatranscriptomics to assess inoculant establishment and functioning. Resident microbiome diversity did not affect total N. linckia gene expression, but heterotrophic DG1 members showed reduced expression in high-diversity soils. Soil diversity and urea history drove broad shifts in DG1 transcription and significantly affected transcription of key N. linckia carbon and nitrogen metabolism genes. High-diversity soils with urea were associated with increased transcription of photosynthesis, CAZyme, and nitrogen cycling genes, whereas low-diversity soils without urea promoted increased nitrogenase transcription and reduced carbon and nitrogen metabolism transcription. These results show that inoculant outcomes depend not only on establishment, but also how soil conditions and biology shape post-establishment functioning.

microbiology↗

bioRxiv2026

Genome-resolved metagenomics reveals abundant novel, non-methanogenic lineages in tropical alpine paramo soils

Wetlands are the largest natural source of atmospheric methane, and tropical wetlands are projected to drive the greatest increase in emissions under climate change, yet high-altitude tropical systems remain largely absent from global frameworks predicting this response. Here, we investigated soil metagenomes from the paramo ecosystem in Chingaza National Natural Park, Colombia, across three ecosites. Microbial community composition differed significantly among ecosites, with peatland soils exhibiting the highest diversity. Genome-resolved metagenomics recovered 109 high-quality metagenome-assembled genomes (MAGs); 8.3% (9 MAGs) could not be assigned to any described genus, representing phylogenetically novel lineages, while 37.6% (41 MAGs) were absent from the wetland-specific MUCC database but present in GTDB. Functional analyses revealed widespread Wood-Ljungdahl pathway potential, complemented by the bacterial reductive glycine pathway and reverse tricarboxylic acid cycle. No methanogenesis marker (mcrABG) was detected in any high- or medium-quality genomes or assembled contigs, identifying the genomically resolved community as non-methanogenic. A read-level search nonetheless recovered a low-abundance methanogen signal concentrated in peatland and affiliated with hydrogenotrophic lineages typical of acidic peatlands, indicating that methanogenesis is present but minor. Metabolic potential instead supported acetogenic carbon fixation and sulfate reduction, suggesting a carbon-cycling regime distinct from canonical methane-dominated wetlands. Together, these findings establish tropical alpine paramos as overlooked reservoirs of phylogenetically novel microbial diversity with metabolic potential distinct from other wetlands. Public release of these MAGs expands genomic representation of tropical alpine ecosystems and provides a foundation for improving predictions of carbon cycling in high-altitude ecosystems.

microbiology↗

bioRxiv2026

Rainfall-induced microbial resuscitation reveals functional decoupling across biocrust succession

Dryland ecosystems rely on infrequent rainfall pulses to activate soil microbial communities, yet the fraction and identity of microbes resuscitating after hydration remain unclear. We applied bioorthogonal non-canonical amino acid tagging coupled with fluorescence-activated cell sorting (BONCAT-FACS) and 16S rRNA gene sequencing to identify translationally active bacteria in early (L-BSC) and late (D-BSC) successional cyanobacteria-dominated biocrusts subjected to simulated rainfall under light and dark conditions. Our results reveal that only a small subset of the microbial community resumes activity within six hours, with higher active cell abundances in mature crusts. Microbial activity patterns were largely independent of light exposure and showed partial decoupling from total community composition, indicating that presence does not predict short-term function. These findings suggest that biocrust maturity shapes microbial activation dynamics and that functional responses to precipitation pulses are governed by a conserved pool of fast responders, informing predictions of dryland soil microbiome resilience under changing precipitation regimes.

ecology↗

bioRxiv2025

Unraveling the diversity and functional potential of cyanosphere microbiomes assembled from terrestrial cyanobacteria

The cyanosphere consists of heterotrophic microorganisms residing within the exopolysaccharide sheath of cyanobacteria, acting as a crucial interface between the cyanobacteria and their surrounding environment. Understanding the interactions between cyanobacteria and their cyanospheres is essential for predicting the success of terrestrial cyanobacteria in providing ecosystem services in nutrient-poor environments. However, knowledge of the microbial diversity within the cyanosphere remains limited. In this study, we employed metagenomic sequencing to reconstruct 410 metagenome-assembled genomes (MAGs) from cyanosphere-associated microbes linked to 56 unialgal terrestrial cyanobacteria cultures, representing 12 distinct cyanobacteria orders. Our findings revealed that the composition of cyanosphere microbial communities was unique to each cyanobacterial host and was significantly shaped by environmental factors such as habitat, precipitation, and temperature from which the cultures were originally obtained. Notably, three microbial genera, Brevundimonas, Devosia, and Sphingopyxis, were present in over 30% of the cyanospheres, forming a core cyanosphere microbiome. Functional gene analysis showed a distinction between the cyanobacteria and their associated cyanospheres, with dissimilatory nitrate reduction being the dominant pathway in the cyanosphere, while nitrogen fixation was more common in the cyanobacteria. Three cyanospheres also contained nitrogen fixation genes of which two hosts were nitrogen fixation capable themselves. The cyanosphere harbored genes for polysaccharide lyases, indicating a possible link to the exopolysaccharides produced by the cyanobacteria. Given the observed variability in microbial community composition and function across different cyanobacterial hosts, future ecological assessments and restoration efforts involving cyanobacteria should not only focus on the cyanobacteria themselves but also consider their associated microbial communities. ImportanceOur study identifies members of a highly understudied, and potentially under-valued, microbial community -- the cyanosphere. We used a diversity of terrestrial cyanobacteria to understand how the cyanosphere composition and predicted functions were influenced by the host cyanobacterium and environmental factors using metagenomics. This is a new approach to study the cyanosphere and provides insights into the diversity of terrestrial microbial communities. Importantly, our results underscore the need to consider microbial consortia when assessing the ecological potential of cyanobacteria in terrestrial restoration.

ecology↗

bioRxiv2024

Genomic evidence for widespread reciprocal recognition and killing among Pseudomonas syringae strains

Community assembly dynamics are in part driven by competition between community members. Diverse bacteria antagonize competitors through the production of toxic compounds, such as bacteriophage-derived tailocins. These toxins are highly specific in their targeting, which is determined by interactions between the tailocins tail fiber and competitors lipopolysaccharide O-antigen moieties. Tailocins play a pivotal role in mediating microbial interactions among the economically significant plant pathogens within the Pseudomonas syringae species complex, with the potential to alter community structure and disease progression in host plants. Previous work looking at 45 P. syringae strains has demonstrated that at least two phylogenetic clades of tail fibers are encoded in the conserved tailocin region across the species complex, which roughly corresponds to two clusters of targeting activity. To better understand the full diversity of tail fibers associated with tailocins in the species complex, we screened 2,161 publicly available genomes for their tailocin tail fiber content, predicted protein structures that represent the diversity of fibers, and investigated forces possibly driving the distribution of fibers throughout the species complex. Here we present evidence that while the two previously described tail fiber clades are indeed widespread among virulent P. syringae strains, their distribution is largely uncorrelated with phylogeny. Instead, we found that the presence of one tail fiber or the other is strongly correlated with the allelic diversity of another gene, associated with lipopolysaccharide O-antigen structure, dTDP-4-dehydrorhamnose reductase. Our findings suggest the presence of two reciprocally targeting groups of strains distributed throughout the P. syringae species complex that transcend phylogenetic relationships.

genomics↗

bioRxiv2023

Positive relationship between substrate-induced respiration rate and translationally active bacteria count in soil

Soil microorganisms carry out many processes that are fundamental to soil functions. Among the millions of microbial cells present in a gram of soil, however, less than 2% are commonly estimated to be active at any point in time. Because the respiratory response of a bulk soil to carbon substrate addition would be expected to reflect the number of active cells, we hypothesized a positive correlation between active cells and soil respiration rates during substrate-induced respiration (SIR) assays. To test this, we monitored respiration and active cell counts during 24-h incubations of agricultural soil subsamples after treating with two carbon substrates or a water-only control. We enumerated active cells with the Bioorthogonal Non-canonical Amino Acid Tagging (BONCAT) method. BONCAT provides a labeled amino acid for active cells to incorporate into newly synthesized proteins, which can then be tagged with a fluorescent dye to enable enumeration by flow cytometry. Both respiration rates and active cell counts increased over time and were positively correlated with each other after 6 h of incubation. After 24 h, increases in active cells were proportionally greater than increases in respiration. Additionally, carbon-amended soils had higher respiration rates than water-only soils with similar active cell counts, suggesting differences in carbon use efficiency. Our study documents for the first time the respiratory response from in-situ microbial activation induced by substrate amendment of soil within 6 h, a short enough timescale to exclude most cell replication. This study also demonstrates that the correlation between active cell numbers and respiration is substrate-dependent. IMPORTANCEWhile many critical ecosystem services provided by soil are known to rely on microbial activity, the soil microbial community largely remains a black box. While respiration is a common indicator of bulk soil microbial activity, this study demonstrates that the relationship between respiration and the number of active cells differs based on available carbon substrates. Advancing knowledge in this area will both enable better interpretation of biological soil tests by land managers and inform researchers modeling contributions of soil microbial respiration to global carbon dynamics.

ecology↗

bioRxiv2022

SYRINGAE: A web-based application for Pseudomonas syringae isolate characterization

The Pseudomonas syringae species complex (PSSC) is a diverse group of plant pathogens with a collective host range encompassing almost every food crop grown throughout the world. As a threat to global food security, rapid detection and characterization of epidemic and emerging pathogenic lineages is essential. However, phylogenetic identification and prediction of virulence is often complicated by an unclarified taxonomy and the diversity of virulence factor repertoires carried by PSSC isolates. To address these issues, we have built SYRINGAE (www.syringae.org), a web-based phylogenetic placement and functional inference pipeline for PSSC. SYRINGAE contains a comprehensive phylogeny of 2,161 quality-checked genome assemblies annotated with 120 virulence genes. From this dataset, naive Baye classification models trained from life identification numbers (LINs) and common marker gene sequences can be used for accurate identification of isolates. SYRINGAE efficiently articulates taxonomical and functional data generated over the last several decades on PSSC and constitutes a unique tool tailored towards the rapid characterization of PSSC emerging strains of concern.

microbiology↗

bioRxiv2022

Evaluation of the taxonomic accuracy and pathogenicity prediction power of 16 primer sets amplifying single copy marker genes in the Pseudomonas syringae species complex

The Pseudomonas syringae species complex is comprised of several closely related species of bacterial plant pathogens. Here, we use in-silico methods to assess 16 PCR primer sets designed for broad identification of isolates throughout the species complex. We evaluate their in-silico amplification rate in 2,161 publicly available genomes, the correlation between pairwise amplicon sequence distance and whole genome average nucleotide identity (ANI), and we train naive Bayes classification models to quantify classification resolution. Further, we show the potential for using single amplicon sequence data to predict an important determinant of host specificity and range, type III effector protein repertoires.

microbiology↗

bioRxiv2018

Study of Oak Ridge soils using BONCAT-FACS-Seq reveals that a large fraction of the soil microbiome is active

The ability to link soil microbial diversity to soil processes requires technologies that differentiate active subpopulations of microbes from so-called relic DNA and dormant cells. Measures of microbial activity based on various techniques including DNA labelling have suggested that most cells in soils are inactive, a fact that has been difficult to reconcile with observed high levels of bulk soil activities. We hypothesized that measures of in situ DNA synthesis may be missing the soil microbes that are metabolically active but not replicating, and we therefore applied BONCAT (Bioorthogonal Non Canonical Amino Acid Tagging) i.e. a proxy for activity that does not rely on cell division, to measure translationally active cells in soils. We compared the active population of two soil depths from Oak Ridge (TN) incubated under the same conditions for up to seven days. Depending on the soil, a maximum of 25 - 70% of the cells were active, accounting for 3-4 million cells per gram of soil type, which is an order of magnitude higher than previous estimates. The BONCAT positive cell fraction was recovered by fluorescence activated cell sorting (FACS) and identified by 16S rDNA amplicon sequencing. The diversity of the active fraction was a selected subset of the bulk soil community. Excitingly, some of the same members of the community were recruited at both depths independently from their abundance rank. On average, 86% of sequence reads recovered from the active community shared >97% sequence similarity with cultured isolates from the field site. Our observations are in line with a recent report that, of the few taxa that are both abundant and ubiquitous in soil, 45% are also cultured - and indeed some of these ubiquitous microorganisms were found to be translationally active. The use of BONCAT on soil microbiomes provides evidence that a large portion of the soil microbes can be active simultaneously. We conclude that BONCAT coupled to FACS and sequencing is effective for interrogating the active fraction of soil microbiomes in situ and provides new perspectives to link metabolic capacity to overall soil ecological traits and processes.

microbiology↗