Biology subjects

Colombet, J.

Publications and source records attributed to Colombet, J..

6 recordsLinked to original sources

bioRxiv2025

Pera virus mimics bacteria to infect Pedopumella sp. a freshwater heterotrophic Chrysophyceae

Heterotrophic Chrysophyceae play a key role in the functioning of many aquatic food webs as primary predators of prokaryotes, but their top-down regulatory factors are poorly understood. To date, no virus isolates from heterotrophic Chrysophyceae have been described in the literature. Here we describe Pera virus, a giant virus infecting the heterotrophic Chrysophyceae Pedospumella sp.. Pera virus have an icosahedral capsid-vesicle morphology, a feature unprecedented in viruses. We hypothesize that this vesicle mimics the shape of bacteria so that the virus is recognized as such by its bacteriophage protist host. This constitutes a morphological evolution of viruses that promotes infection of their heterotrophic host. The capside measures 414 nm in diameter. The vesicle has a variable diameter ranging from 231 to 587 nm. The virion as a whole can reach 1008 nm in length. We searched for this new type of virus under environmental conditions during time series studies in hyper-eutrophic freshwater lakes. Surprisingly, we report the existence of Pera virus-like particles (PVLs) of various shapes and size that can reach 5 {micro}m illustrating the hidden diversity of this undescribed virus types. The dynamics of PVLs, which can reach 2.4 x 105 PVL.mL-1, are closely associated with those of unicellular heterotrophic eukaryotes, acting as major regulatory agents of protozoan bacterivory in freshwater. This pair provides a new model for understanding the evolution of giant viruses and their ecological role.

ecology↗

bioRxiv2025

Non-living respiration: another breath in the soil?

The present study challenges the traditional view that respiration of organic carbon to CO2 is exclusively an intracellular process, revealing that organic compound respiration can occur spontaneously in an extracellular context in soils. Using 1H nuclear magnetic resonance spectroscopy to analyse the dynamics of the sterile soil exometabolomes alongside C-CO2 flux analyses and sterile soil fuel cells, we show that soil catalysts facilitate a diverse array of substrate-driven reactions, leading to the complete oxidation of organic compounds to CO2 with O2 consumption. Our results indicate that soil particles are capable of transferring electrons from substrates to the final acceptor, sustaining metabolic processes independently of living cells. Notably, some soil catalysts and induced respiration remain stable for over six years. Our results support the coexistence of cellular and non-cellular metabolic pathways in soil respiration.

ecology↗

bioRxiv2024

Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments

The discovery of Jumbo phages and giant viruses of microeukaryotes has transformed our perception of the virosphere. Metagenomic and metatranscriptomic data further highlight their diversity and ecological impact. Nevertheless, sequence-based approaches fail to take into account the morphological diversity of non-cultivated viruses, resulting in our fragmented understanding of their nature and role in the environment. Here, we combined flow cytometry and electron microscopy to uncover both previously unsuspected morphological diversity as well as significant abundances of large viruses in aquatic environments. We discovered four new viral morphotypes, all of which were associated with microeukaryotes. We also obtained insights into the multi-year dynamics of the abundances of both giant microeukaryotic viruses and Jumbo phages. This work deepens our understanding of large viruses and reveals their key role as regulators of microbial communities.

ecology↗

bioRxiv2022

Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin

Permanently stratified lakes contain diverse microbial communities that vary with depth, and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined. Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. Overall, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments. Thus, environmental gradients in Lac Pavin probably select for the capacities of CPR bacteria and phages to a lesser extent than other bacteria and archaea, possibly because selection on the former groups is indirect and depends on host characteristics.

microbiology↗

bioRxiv2021

Long-term incubation of lake water enables genomic sampling of consortia involving Planctomycetes and Candidate Phyla Radiation bacteria

Microbial communities in lakes can profoundly impact biogeochemical processes through their individual activities and collective interactions. However, the complexity of these communities poses challenges, particularly for studying rare members. Laboratory enrichments can select for subsystems of interacting organisms and enable genome recovery for enriched populations. Here, a reactor inoculated with water from Lake Fargette, France, and maintained under dark conditions at 4{degrees}C for 31 months enriched for diverse Planctomycetes and Candidate Phyla Radiation (CPR) bacteria. We reconstructed draft genomes and predicted metabolic traits for 12 diverse Planctomycetes and 9 CPR bacteria, some of which are likely representatives of undescribed families or genera. One CPR genome representing the little-studied lineage Peribacter (1.239 Mbp) was curated to completion, and unexpectedly, encodes the full gluconeogenesis pathway. Metatranscriptomic data indicate that some Planctomycetes and CPR bacteria were active under the culture conditions. We also reconstructed genomes and obtained transmission electron microscope images for numerous phages, including one with a >300 kbp genome and several predicted to infect Planctomycetes. Together, our analyses suggest that freshwater Planctomycetes may act as hubs for interaction networks that include symbiotic CPR bacteria and phages.

microbiology↗

bioRxiv2020

Unveiling Crucivirus Diversity by Mining Metagenomic Data

The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding ssDNA (CRESS-DNA) viruses that encode capsid proteins (CPs) that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of CP genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and ten CP-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins, and that the exchange of Rep protein domains between cruciviruses is rarer than gene exchange. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses. IMPORTANCEViruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and are viruses that appear to have multiple origins from prokaryotic plasmids. CRESS-DNA viruses such as the cruciviruses, have homologues of capsid proteins (CPs) encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability.

evolutionary biology↗