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Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria
Stefan M Neuenschwander1, Rohit Ghai2, Jakob Pernthaler1
1Limnological Station, Institute of Microbial and Plant Biology, University of Zurich, Zurich, Switzerland.
The ISME Journal
|October 14, 2017
Summary
Newly cultured freshwater Actinobacteria reveal streamlined genomes and metabolic diversity. This microdiversification may explain their abundance and success in dynamic aquatic environments.
Area of Science:
- Microbiology
- Genomics
- Environmental Science
Background:
- Actinobacteria of the acI lineage are abundant in freshwater but lack pure cultures, hindering genomic study.
- Metabolic dependencies on other microbes may explain the lack of axenic cultures.
Purpose of the Study:
- To present genomes from 16 axenic cultures of acI Actinobacteria.
- To investigate the genomic basis for their environmental success.
- To understand their metabolic diversity and evolutionary adaptations.
Main Methods:
- Isolation and cultivation of acI Actinobacteria.
- Whole-genome sequencing of 16 isolates.
- Comparative genomic analysis of metabolic pathways and genome reduction.
Main Results:
- 16 axenic cultures of acI Actinobacteria were established, exhibiting minute cell size and streamlined genomes (1.2-1.4 Mbp) with low GC content.
- Genome reduction suggests auxotrophy, supporting the 'Black Queen' hypothesis.
- Significant inter- and intraspecific metabolic diversity, particularly in carbohydrate metabolism encoded in genomic islands, was observed.
Conclusions:
- The microdiversification of acI Actinobacteria genotypes likely contributes to their success in dynamic freshwater ecosystems.
- A new order, 'Candidatus Nanopelagicales,' with two new genera and nine new species, is proposed based on genomic data.