ArticleThe ISME journal2024
Flexible genomic island conservation across freshwater and marine Methylophilaceae.
Article in The ISME journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Application potential of a marine-derived halotolerant yeast in saline azo dye wastewater treatment: elucidating degradation pathways and osmo-adaptive strategies.Bioprocess and biosystems engineering · 2026Article
- Lotus-fish co-culture reshapes pond microbiota and improves ecological stability relative to fish monoculture.Frontiers in microbiology · 2026Article
- Illuminating the newly produced viruses within the virosphere with bioorthogonal noncanonical amino acid tagging and single-virus genomic sequencing technologies.ISME communications · 2026Article
- Article
- Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium.Nature microbiology · 2025Article
- Bringing the uncultivated microbial majority of freshwater ecosystems into culture.Nature communications · 2025Article
- Novel and diverse features identified in the genomes of bacteria isolated from a hydrothermal vent plume.Applied and environmental microbiology · 2025Article
- Biodegradation of S-Triazine Herbicides Under Saline Conditions byMicroorganisms · 2025Article
- Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales.mBio · 2025Article
- Plateau Pika Disturbance Changes Soil Bacterial Functions and Exoenzyme Abundance to Modulate the C Cycle Pathway in Alpine Grasslands.International journal of molecular sciences · 2024Article
- Global freshwater distribution of Telonemia protists.The ISME journal · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
9 authors.
Funding
Abstract
The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.
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