Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

Abstract

Evolutionary transitions between fresh and salt water happen infrequently among bacterioplankton. Within the ubiquitous and highly abundant heterotrophic Alphaproteobacteria order Pelagibacterales (SAR11), most members live in marine habitats, but the LD12 subclade has evolved as a unique freshwater lineage. LD12 cells occur as some of the most dominant freshwater bacterioplankton, yet this group has remained elusive to cultivation, hampering a more thorough understanding of its biology. Here, we report the first successful isolation of an LD12 representative, strain LSUCC0530, using high-throughput dilution-to-extinction cultivation methods, and its complete genome sequence. Growth experiments corroborate ecological data suggesting active populations of LD12 in brackish water up to salinities of ~5. LSUCC0530 has the smallest closed genome thus far reported for a SAR11 strain (1.16 Mbp). The genome affirms many previous metabolic predictions from cultivation-independent analyses, like a complete Embden–Meyerhof–Parnas glycolysis pathway, but also provides novel insights, such as the first isocitrate dehydrogenase in LD12, a likely homologous recombination of malate synthase from outside of the SAR11 clade, and analogous substitutions of ion transporters with others that occur throughout the rest of the SAR11 clade. Growth data support metagenomic recruitment results suggesting temperature-based ecotype diversification within LD12. Key gene losses for osmolyte uptake provide a succinct hypothesis for the evolutionary transition of LD12 from salt to freshwater. For strain LSUCC0530, we propose the provisional nomenclature Candidatus fonsibacter ubiquis.

Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake

“…LD12 (Ca. Fonsibacter) is a freshwater division of the SAR11 lineage (Pelagibacteraceae), which is one of the most ubiquitous and abundant bacterioplankton in freshwater, as is the case for its marine counterparts (Salcher et al, 2011;Henson et al, 2018). Indeed, LD12 was by far the most abundant LBMAG in the epilimnion throughout the study period (Supporting Information Table S4).…”

“…However, despite a growing number of viromic studies in freshwater systems (Skvortsov et al, 2016;Moon et al, 2017;Silva et al, 2017;Arkhipova et al, 2018), viruses infecting other typical freshwater bacterioplankton lineages, such as LD12 (Ca. Fonsibacter) (Henson et al, 2018) and Limnohabitans (Kasalický et al, 2013) have yet to be characterized. Moreover, no viromic study has investigated an oxygenated hypolimnion, leaving hypolimnetic viral diversity and virus-host interactions totally unexplored.…”

Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake

“…However, viruses infecting other typical freshwater bacterioplankton lineages, such as LD12 (Ca. Fonsibacter) (68,69) and Limnohabitans (70) have yet to be characterized. Moreover, despite the ecological and biogeochemical importance of the microbial community of the oxygenated hypolimnion, as described above, no viromics research has been performed in this realm, leaving hypolimnetic viral diversity and virus-host interactions totally unexplored.…”

Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy

“…There is also a more recent case of an ubiquitous oil-degrading organism that was first observed based on metagenomes and was subsequently isolated in pure culture due to its apparent important role in oil biodegradation (Karthikeyan et al, 2019). There are many more examples in the literature where the knowledge of uncultured and ecologically relevant microorganisms led to their isolation (Stott et al, 2008;Harbison et al, 2016;Henson et al, 2018;Lee et al, 2019), and the successful application of novel metagenome-guided cultivation methods (Tyson et al, 2005;Karthikeyan et al, 2019;Zhang et al, 2019). We are convinced that the in-depth taxonomic description of yet-uncultured prokaryotic clades will actually make continued isolation efforts more relevant due to potential economic benefits (Keller and Zengler, 2004), and the personal satisfaction from cultivating not any bacterium, but a 'missing' candidate taxon (Pandit and Rahalkar, 2019).…”