Long-Term Incubation of Lake Water Enables Genomic Sampling of Consortia Involving <i>Planctomycetes</i> and Candidate Phyla Radiation Bacteria - Archive ouverte HAL Access content directly
Journal Articles mSystems Year : 2022

Long-Term Incubation of Lake Water Enables Genomic Sampling of Consortia Involving Planctomycetes and Candidate Phyla Radiation Bacteria

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Abstract

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 organisms such as Candidate Phyla Radiation bacteria (CPR) and enigmatic entities such as aster-like nanoparticles (ALNs). Here, a reactor was inoculated with water from Lake Fargette, France, and maintained under dark conditions at 4°C for 31 months and enriched for ALNs, diverse Planctomycetes, and 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 "Candidatus Peribacter" was curated to completion (1.239 Mbp) and unexpectedly encodes the full gluconeogenesis pathway. Metatranscriptomic data indicate that some planctomycetes and CPR bacteria were active under the culture conditions, accounting for ;30% and ;1% of RNA reads mapping to the genome set, respectively. We also reconstructed genomes and obtained transmission electron microscope images for numerous viruses, including one with a .300-kbp genome and several predicted to infect Planctomycetes. Together, our analyses suggest that freshwater Planctomycetes are central players in a subsystem that includes ALNs, symbiotic CPR bacteria, and viruses. IMPORTANCE Laboratory incubations of natural microbial communities can aid in the study of member organisms and their networks of interaction. This is particularly important for understudied lineages for which key elements of basic biology are still emerging. Using genomics and microscopy, we found that members of the bacterial lineage Planctomycetes may be central players in a subset of a freshwater lake microbiome that includes other bacteria, archaea, viruses, and mysterious entities, called aster-like nanoparticles (ALNs), whose origin is unknown. Our results help constrain the possible origins of ALNs and provide insight into possible interactions within a complex lake ecosystem. KEYWORDS CPR bacteria, aster-like nanoparticles, lake microbiome, metagenomics, viruses F reshwater lakes host diverse microbial communities that likely control ecosystem biogeochemistry (1, 2). Here, we established a laboratory culture based on an inoculum from Lake Fargette, France, a site chosen as part of a parallel study of enigmatic aster-like nanoparticles (ALNs) (3, 4). ALNs are enigmatic, organic, femtoplankton entities that exhibit bloom-like behavior in various freshwater and coastal environments (3, 4). In this experiment, Editor
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Dates and versions

hal-03865093 , version 1 (22-11-2022)

Licence

Attribution - CC BY 4.0

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Alexander L Jaffe, Maxime Fuster, Marie C Schoelmerich, Lin-Xing Chen, Jonathan Colombet, et al.. Long-Term Incubation of Lake Water Enables Genomic Sampling of Consortia Involving Planctomycetes and Candidate Phyla Radiation Bacteria. mSystems, 2022, 7 (2), ⟨10.1128/msystems.00223-22⟩. ⟨hal-03865093⟩
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