Biology subjects

Pelletier, D. A.

Publications and source records attributed to Pelletier, D. A..

9 recordsLinked to original sources

bioRxiv2026

Data coherence over data volume drives generalisable genome-based prediction of microbial carbon utilisation

Microbial carbon utilisation is a foundational ecological phenotype that remains difficult to predict from genomes despite well-characterised pathways. Machine-learning models generalise poorly across datasets, a failure usually attributed to training-set size and taxonomic bias. To test this, we integrated binary growth phenotypes for 819 strains across 240 carbon sources from four datasets. Balanced accuracy fell from 0.86 within datasets to 0.62 across them, and testing on close relatives recovered only 0.03 of that drop, so mechanistically inconsistent genotype-phenotype relationships drove models to dataset-correlated shortcuts. Restricting training to concordant samples (measured growth matched their annotated pathway) doubled the carbon sources recovering known pathway genes across datasets (6 to 12 of 15), whereas matched random subsets did not. Adding over 8000 literature-curated BacDive genomes to the training set did not improve cross-dataset performance more than the smaller concordant set, suggesting coherence matters more than volume. Because such filtering requires a mechanistic predictor, we tested a mechanism-free alternative combining phylogenetic agreement and experimental labels, which recovered part of the gain but not the recall advantage. Concordance-trained models were bounded specialists, rescuing mechanistic false negatives twice as often as false positives (44\% versus 19\%), mostly metabolic generalists. To locate those bounds, model confidence defined an applicability domain, and prioritising low-confidence genomes for training improved cross-dataset accuracy more than random or diversity-based sampling, especially for the weaker phenotypes. This recasts generalisation in biological machine learning as a problem of label-mechanism agreement and applicability-domain definition, alongside data volume and algorithm choice.

bioinformatics↗

bioRxiv2025

Populus trichocarpa associated microbiomes vary across a natural temperature, elevation and rainfall gradient

Abiotic stresses associated with warming and drought are increasing in frequency and severity due to climate change. However, microbial associations can partially mitigate their adverse effects on plant physiology. We examined the bacterial/archaeal and fungal communities with 16S rRNA and ITS2 gene region amplicon sequencing of bulk soil, rhizosphere soil, and root endosphere samples of Populus trichocarpa trees from 11 sites along a 200 km transect with highly variable precipitation, temperature, and soil conditions over the Cascade Mountains in Washington, USA. Foliar stress response was examined with qRT-PCR and field physiological measurements. Soil conditions were examined with physiochemical sample analysis and site climate conditions were approximated using DAYMET. For each niche sampled, bacterial/archaeal and fungal communities clustered into three distinct micro-climate groups: a high-precipitation, low-stress community on the western side of the range, and two stressed climate communities: a high-elevation community nearer the crest of the pass, and a warmer and drier community along the eastern slope. The differences between these micro-climate communities, though still distinct, were notably diminished within the P. trichocarpa root endosphere, indicating that P. trichocarpa likely has a homogenizing effect on the microbiome under stress, but climate plays a major role in shaping these microbial communities.

ecology↗

bioRxiv2025

Microbial Modulation of Host Plant Proteasome Activity Improves Heat Stress Tolerance

Global climate change marked by rising temperatures and increasingly frequent, severe heat waves, threatens plant health, productivity, and ecosystem function. Beneficial plant-microbe associations are increasingly recognized for their role in mitigating abiotic stress, yet the molecular mechanisms underlying microbially-conferred thermotolerance remain poorly understood. Here, we developed a population-based assay using Sphagnum peat mosses, a key species in peatland ecosystems that sequester 33-50% of the worlds soil carbon as recalcitrant peat, to perform microbiome transfers and assess microbial contributions to heat resilience. Strain-based assays in Sphagnum and Arabidopsis identified Variovorax as a key thermotolerance-enhancing microbe and identified ECM29, a proteasome-associated protein, as critical for this interaction. In Arabidopsis, Variovorax sp. CF313 association led to ECM29 preferentially binding the RPT1 subunit of the 19S regulatory particle, inhibiting 20S proteasome gate opening and slightly reducing proteasomal activity. This results in the accumulation of ubiquitinated proteins and induces HSP70 transcription, priming the host for heat shock stress even in the absence of prior heat exposure. These findings establish ECM29 as a key regulator of proteasome activity in response to microbial interactions, highlighting a previously unknown mechanism by which microbes enhance plant thermotolerance. More broadly, this work highlights the importance of leveraging natural systems and ecologically relevant models to identify strategies for enhancing plant and ecosystem resilience to a changing climate. Significance StatementGlobal climate change poses severe threats to plant health and productivity, with cascading impacts on ecosystems. Beneficial plant-microbe interactions offer promising strategies to mitigate abiotic stress, yet the molecular mechanisms often remain unclear. This study uncovers a novel thermotolerance mechanism mediated by Variovorax modulating the plant host proteasome. Using a QTL derived from Sphagnum peat mosses, and tested within a genetically tractable Arabidopsis model, we identified ECM29, a highly conserved protein across diverse plant species, as a key regulator of proteasome activity. ECM29 primes plants for heat stress by inducing HSP70 transcription through proteasome modulation. Additionally, we demonstrated that ECM29 is required for the host to receive microbially conferred thermotolerance, but is not necessary for innate priming to heat stress. These findings highlight the potential of leveraging natural systems and ecologically relevant species to develop innovative genetic models, advancing plant resilience and productivity in a warming world.

plant biology↗

bioRxiv2025

BONCAT-Live for isolation and cultivation of active environmental bacteria

In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including in association with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating the individual microbes that respond to specific changes has been difficult. To address that, we implemented BONCAT-Live, by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient enriched conditions. From a Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human oral microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities. ImportanceDynamic microbial activity transforms environments and impacts health and disease in associations with plants and animals, including humans. Identifying the contribution of individual microbes to those processes in real time has not been generally compatible with their selective cultivation. BONCAT-Live tracks which microbes in environmental samples are translationally active and couples it with single cell isolation and cultivation. By studying the response of individual community member to specific natural or induced physical or chemical changes in the environment and culturing those organisms, BONCAT-Live enables further insights into microbial metabolic strategies, community dynamics and environmental adaptations.

microbiology↗

bioRxiv2024

Predation by a ciliate community mediates temperature and nutrient effects on a peatland prey prokaryotic community.

Temperature significantly impacts microbial communities composition and function, which plays a vital role in the global carbon cycle that determines climate change. Nutrient influxes often accompany rising temperatures due to human activity. While ecological interactions between different microorganisms could shape their response to environmental change, we do not understand how predation may influence these responses in a warmer and increasingly nutrient-rich world. Here, we assess whether predation by a ciliate community of bacterial consumers influences changes in the diversity, biomass, and function of a freshwater prokaryotic community under different temperature and nutrient conditions. We found that predator presence mediates the effects of temperature and nutrients on total prokaryotic community biomass and composition through various mechanisms, including direct and indirect effects. However, the total community function was resilient. Our study supports previous findings that temperature and nutrients are essential drivers of microbial community composition and function but also demonstrates how predation can mediate these effects, indicating that the biotic context is as important as the abiotic context to understanding microbial responses to novel climates. ImportanceWhile the importance of the abiotic environment in microbial communities has long been acknowledged, how prevalent ecological interactions like predation may influence these microbial community responses to shifting abiotic conditions is largely unknown. Our study addresses the complex interplay between temperature, nutrients, predation, and their joint effects on microbial community diversity and function. Our findings suggest that while temperature and nutrients are fundamental drivers of microbial community dynamics, the presence of predators significantly alters these responses. Our study underscores the impact of abiotic factors on microbial communities and the importance of accounting for the biotic context in which these occur to understand, let alone predict, these responses properly.

ecology↗

bioRxiv2023

Climate Change Factors Interact to Shift Functional Microbial Composition in Peatlands

Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria, fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2 could alter the structure and function of peatland microbial food webs -- a fragile ecosystem that stores 25% of terrestrial carbon and is increasingly threatened by human exploitation.

ecology↗

bioRxiv2020

Sphagnum peat moss thermotolerance is modulated by the microbiome

Sphagnum peat mosses is a major genus that is common to peatland ecosystems, where the species contribute to key biogeochemical processes including the uptake and long-term storage of atmospheric carbon. Warming threatens Sphagnum mosses and the peatland ecosystems in which they reside, potentially affecting the fate of vast global carbon stores. The competitive success of Sphagnum species is attributed in part to their symbiotic interactions with microbial associates. These microbes have the potential to rapidly respond to environmental change, thereby helping their host plants survive under changing environmental conditions. To investigate the importance of microbiome thermal origin on host plant thermotolerance, we mechanically separated the microbiome from Sphagnum plants residing in a whole-ecosystem warming study, transferred the component microbes to germ-free plants, and exposed the new hosts to temperature stress. Although warming decreased plant photosynthesis and growth in germ-free plants, the addition of a microbiome from a thermal origin that matched the experimental temperature completely restored plants to their pre-warming growth rates. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure, including the composition of key cyanobacteria symbionts, in a manner that induced the plant heat shock response, especially the Hsp70 family and jasmonic acid production. The plant heat shock response could be induced even without warming, suggesting that the warming-origin microbiome provided the host plant with thermal preconditioning. Together, our findings show that the microbiome can transmit thermotolerant phenotypes to host plants, providing a valuable strategy for rapidly responding to environmental change.

plant biology↗

bioRxiv2018

Diversity of active viral infections within the Sphagnum microbiome

Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of 6 Sphagnum plants were obtained from a peatland in northern Minnesota and total RNA extracted and sequenced. Metatranscriptomes were assembled and contigs screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein, gp23, as a marker for phage diversity, we identified 33 contigs representing undocumented phage s that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) major capsid protein were used as markers for ssRNA viruses and NCLDV, respectively. In total 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent near-complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinto-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades, and suggest viruses may play a considerable role in the ecology of the Sphagnum microbiome.\n\nSignificanceSphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor its own growth over other plant species. This slows rates of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the mosss growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome, and identifying new potential model systems to study virus-host interactions in the peatland ecosystem.

microbiology↗

bioRxiv2017

Experimental warming reduces the diversity and functional potential of the Sphagnum microbiome

Climate change may reduce biodiversity leading to a reduction in ecosystem productivity. Despite numerous reports of a strong correlation of microbial diversity and ecosystem productivity, little is known about the warming effects on plant associated microbes. Here we explore the impact of experimental warming on the microbial and nitrogen-fixing (diazotroph) community associated with the widespread and ecologically relevant Sphagnum genus in a field warming experiment. To quantify changes in the abundance, diversity, and community composition of Sphagnum microbiomes with warming we utilized qPCR and Illumina sequencing of the 16S SSU rRNA and nifH gene. Microbial and diazotroph community richness and Shannon diversity decreased with warming (p<0.05). The diazotroph communities shifted from diverse communities to domination by primarily Nostocaceae (25% in control samples to 99% in elevated temperature samples). In addition, the nitrogen fixation activity measured with the acetylene reduction assay (ARA) decreased with warming treatment. This suggests the negative correlation of temperature and microbial diversity corresponds to a reduction in functional potential within the diazotroph community. The results indicate that climate warming may alter the community structure and function in peat moss microbiomes, with implications for impacts to host fitness and ecosystem productivity, and carbon uptake potential of peatlands.

ecology↗