ArticleThe ISME journal2019
Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae.
Article in The ISME journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed, 118 citations in OpenAlex.
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- From soils to lake: interplay between hydrology and local environmental settings drives species selection across a karst landscape.Frontiers in microbiology · 2026Article
- Diversity of Bacteria.Progress in molecular and subcellular biology · 2026Review
- Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.Microbiome · 2025Article
- Nitrogen-fixing microbes gain genes in diverse types of living environments.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- First Insight into the Natural Attenuation of Emerging Contaminants Using a Metagenomics Approach from Drinking Water Sources in the Free State.Microorganisms · 2025Article
- 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
- Proteomic evidence for aerobic methane production in groundwater by methylotrophic Methylotenera.The ISME journal · 2025Article
- Glacier influence shapes the genomic architecture of the downstream aquatic microbiome.ISME communications · 2025Article
- Purifying selection and low recombination facilitated sequential colonization of benthic and pelagic coastal ocean by ammonia-oxidizing archaea.ISME communications · 2025Article
- GmAMT2.1/2.2-dependent ammonium nitrogen and metabolites shape rhizosphere microbiome assembly to mitigate cadmium toxicity.NPJ biofilms and microbiomes · 2024Article
- Genome streamlining in Parcubacteria transitioning from soil to groundwater.Environmental microbiome · 2024Article
- (Pan)genomic analysis of twoMicrobiology spectrum · 2024Article
- Lineage-specific evolution ofApplied and environmental microbiology · 2024Article
- Flexible genomic island conservation across freshwater and marine Methylophilaceae.The ISME journal · 2024Article
- Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria.The ISME journal · 2024Article
- Ubiquitous genome streamlinedISME communications · 2024Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters ("Ca. Methylopumilus") and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteria), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or is encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome streamlining as such a collection of evolutionarily related microbes from different habitats is rare in the microbial world.
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