Isolation, cultivation, and genome analysis of proteorhodopsin-containing SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322

Seasonal niche differentiation between evolutionary closely related marine bacteria

“…The groups with all ASVs being seasonal could present more constrained optimal conditions of growth than the groups that appear randomly or all year-round. Examples of this behavior are the Puniceispirillales (SAR116 clade), a group harboring proteorhodopsin (Lee et al, 2019) and with most of the ASVs being seasonal and peaking during summer (Lee et al, 2019). Metagenomic and genome-centric approaches as well as physiological experimentation with available isolates would help shedding some light on the traits that determine the niche for these cohesive groups and the differences with other more diverse groups.…”

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).…”

Towards culturing the microbe of your choice

“…All of these methods and more continue to bring thousands of microbes into culture from a variety of systems every year (Thrash, 2019), and announcements of important taxa being cultured for the first time maintains a steady drumbeat (e.g., just in aquatic microbiology: Rappé et al ., 2002; Cho et al ., 2004; Hahn et al ., 2004; Könneke et al ., 2005; Stingl et al ., 2007; Giovannoni et al ., 2008; Eloe et al ., 2011; Baelum et al ., 2012; Marshall and Morris, 2013; Cao et al ., 2014; Durham et al ., 2014; Santoro et al ., 2015; van Kessel et al ., 2015; Ahlgren et al ., 2017; Shah et al ., 2017; Henson et al ., 2018, 2020; Imachi et al ., 2019, 2020; Lee et al ., 2019a; Kim et al ., 2019; Yu and Leadbetter, 2020). Can we do better?…”